System and method for conducting an assay

ABSTRACT

An automated method for analyzing a plurality of samples within a housing of a self-contained system. The system is loaded with a plurality of samples, after which a first assay is performed on a first sample subset and a second assay performed on a second sample subset. The two assays include exposing the samples to a target capture reagent having a solid support for directly or indirectly immobilizing a target nucleic acid that may be present in one or more of the samples. The two assays may be performed with the same or different target capture reagents and target nucleic acids, but the receptacles for performing the exposing step have substantially identical geometries. Following the exposing step, an amplification reaction for amplifying a region of the target nucleic acid is performed with each sample. The amplification reactions of the two assays are performed in receptacles having different geometries.

CROSS-REFERENCE TO RELATED APPLICATIONS

This is a continuation application claiming the benefit under 35 U.S.C.§ 120 of the filing date of U.S. application Ser. No. 15/675,206, filedAug. 11, 2017, which is a continuation application claiming the benefitunder 35 U.S.C. § 120 of the filing date of U.S. application Ser. No.14/213,900, filed Mar. 14, 2014, now U.S. Pat. No. 9,732,374, whichclaims the benefit under 35 U.S.C. § 119(e) of the filing date ofprovisional patent application Ser. No. 61/784,994 filed Mar. 14, 2013,the disclosures of which are incorporated herein by reference.

FIELD

The present disclosure relates to diagnostic systems and methods forperforming a plurality of different molecular assays on a plurality ofsamples and, particularly, molecular assays that comprise target nucleicacid amplification reactions.

BACKGROUND

None of the references described or referred to herein are admitted tobe prior art to the claimed invention.

Molecular assays are nucleic acid-based tests that are used in clinicaldiagnosis, screening, monitoring, industrial and environmental testing,health science research, and other applications to detect the presenceor amount of an analyte of interest in a sample, such as a microbe orvirus, or to detect genetic abnormalities or mutations in an organism.Molecular assays enabling quantification may permit practitioners tobetter calculate the extent of infection or disease and to determine thestate of a disease over time. Quantitative molecular assays are alsouseful for monitoring the effectiveness of a therapy. A variety of knownmolecular assays can be employed to detect various diagnosticindicators.

Molecular assays generally include multiple steps leading to thedetection or quantification of a target nucleic acid in a sample.Targeted nucleic acids often include a region that is specific to anidentifiable “group” of organisms or viruses, where the group is definedby at least one shared sequence of nucleic acid that is common to allmembers of the group and is specific to the group in the particularsample being assayed. Examples of nucleic acid-based detection methodsare disclosed by Kohne in U.S. Pat. No. 4,851,330 and Hogan et al. inU.S. Pat. No. 5,541,308.

Most molecular assays include a detection step in which the sample isexposed to a detection probe or amplification primer that is designed orselected to exhibit specificity under the particular conditions of usefor a nucleic acid sequence belonging to an organism or virus ofinterest. The detection probe or amplification primer can be labeled fordetection with a reporter moiety, such as a chemiluminescent orfluorescent agent, or an intercalating dye can be used toindiscriminately detect the presence of double-stranded nucleic acids ina sample. See, e.g., Livak et al. in U.S. Pat. No. 5,538,848, Hogan etal. in U.S. Pat. No. 5,541,308, Tyagi et al. in U.S. Pat. No. 5,925,517,Higuchi in U.S. Pat. No. 5,994,056, Wittwer et al. in U.S. Pat. No.6,174,670, Whitcombe et al. in U.S. Pat. No. 6,326,145, and Wittwer etal. in U.S. Pat. No. 6,569,627. To render a nucleic acid available forhybridization to the detection probe or amplification primer, cells maybe lysed or permeabilized by a variety of known techniques, including bychemical (e.g., detergent), mechanical (e.g., sonication), and/orthermal procedures. See, e.g., Clark et al. in U.S. Pat. No. 5,786,208.

Before or after exposing a target nucleic acid to a detection probe oramplification primer, the target nucleic acid can be immobilized on asolid support (e.g., particles or beads comprising amagnetically-responsive material) that directly or indirectly binds thetarget nucleic acid. A solid-phase extraction method for directlybinding nucleic acids onto silica beads in the presence of a chaotropicsubstance is described by Boom et al. in U.S. Pat. No. 5,234,864. Anexample of indirect immobilization is described Weisburg et al. in U.S.Pat. No. 6,534,273, which discloses the use of a capture probe thatbinds to the target nucleic acid under a first set of sample conditionsand to an oligonucleotide covalently attached to the solid support undera second set of sample conditions. If the solid support comprises amagnetically-responsive particle or bead, magnets can be used to attractthe solid support to the side of a receptacle containing the solidsupport. Once the immobilized target nucleic acid is isolated within thereceptacle, the isolated target nucleic acid can be separated from atleast a portion of the fluid contents of the sample by, for example,contacting and aspirating the fluid contents of the receptacle with arobotic pipettor or other substance transfer device. See, e.g., Ammannet al. in U.S. Pat. No. 6,605,213. One or more wash steps with abuffered solution or water may be performed to further purify theisolated nucleic acid.

To increase the sensitivity of an assay, a target nucleic acid can beamplified by a nucleic acid amplification reaction, many of which arewell known in the art. Known methods of amplification include PolymeraseChain Reaction (“PCR”) (see, e.g., Mullis et al. in U.S. Pat. Nos.4,683,195, 4,683,202 and 4,800,159; and Mullis et al., Methods inEnzymology, 155:335-350 (1987)); Strand Displacement Amplification(“SDA”) (see, e.g., Walker, PCR Methods and Applications, 3:25-30(1993); Walker et al., Nucleic Acids Res., 20:1691-1996 (1992); andWalker et al., Proc. Natl. Acad. Sci., 89:392-396 (1991)); Ligase ChainReaction (“LCR”) (see, e.g., Birkenmeyer in U.S. Pat. No. 5,427,930 andCarrino et al., in U.S. Pat. No. 5,686,272); and transcription-basedmethods of amplification (Boothroyd et al. in U.S. Pat. No. 5,437,990;Kacian et al., in U.S. Pat. Nos. 5,399,491 and 5,480,784; Davey et al.in U.S. Pat. No. 5,409,818; Malek et al. in U.S. Pat. No. 5,130,238; andGingeras et al. in International Publication Nos. WO 88/01302 and WO88/10315). A review of many amplification reactions, including PCR andTranscription-Mediated Amplification (“TMA”), is provided in Lee et al.,Nucleic Acid Amplification Technologies, BioTechniques Books (1997).

PCR is the oldest and most common form of amplification. Like otheramplification methods, PCR amplifies one or more copies of a region ofnucleic acid by several orders of magnitude, generating thousands tomillions of copies of a particular nucleic acid sequence. PCR has broadapplications in clinical and biological research labs. The uses of thisprocedure are too enumerable, and well known at this time, to recite inthis patent application.

PCR employs thermal cycling, which consists of repeated cycles ofheating and cooling of a reaction mixture. The reaction is generallyinitiated with primers (short DNA fragments containing sequencescomplementary to the target nucleic acid region), along with enzymes andadditional reaction materials. Once under way, the replicated nucleicacid can be used as an additional template in the amplificationreaction, thereby leading to the exponential amplification of a targetnucleic acid sequence.

Because a probe hybridizes to the targeted sequence, the strength of asignal associated with the probe is proportional to the amount of targetnucleic acid sequence that is present in a sample. Accordingly, byperiodically measuring, during the amplification process, a signalindicative of the presence of amplicon, the growth of amplicon over timecan be detected. Based on the data collected during this “real-time”monitoring of the amplification process, the amount of the targetnucleic acid that was originally in the sample can be ascertained. Inone context, collecting data in “real-time” means collecting data whilea reaction or other process is in progress, as opposed to collectingdata at the conclusion of the reaction or process. Systems and methodsfor real-time detection and for processing real-time data to ascertainnucleic acid levels are disclosed by, for example, Lair et al. in U.S.Pat. No. 7,932,081.

To detect different nucleic acids in a single assay, distinct probes maybe designed or selected to separately hybridize to the different nucleicacids, where the probes may include reporter moieties that can bedifferentiated from each other. See, e.g., Livak et al. in U.S. Pat. No.5,538,848, Tyagi et al. in U.S. Pat. No. 5,925,517, Morrison in U.S.Pat. No. 5,928,862, Mayrand in U.S. Pat. No. 5,691,146, and Becker etal. in U.S. Pat. No. 5,928,862. For example, different probes designedor selected to hybridize to different targets can have fluorophores thatfluoresce at a predetermined wavelength when exposed to excitation lightof a prescribed excitation wavelength. Assays for detecting differenttarget nucleic acids can be performed in parallel by alternatelyexposing the sample material to different excitation wavelengths anddetecting the level of fluorescence at the wavelength of interestcorresponding to the probe for each target nucleic acid during thereal-time monitoring process. Parallel processing can be performed usingdifferent signal detecting devices configured to periodically measuresignal emissions during the amplification process, and with differentsignal detecting devices being configured to generate excitation signalsof different wavelengths and to measure emission signals of differentwavelengths.

SUMMARY

Aspects of the present disclosure are embodied in systems, apparatuses,and processes that, inter alia, enhance the functionality of certaindiagnostic first modules by supporting processing capabilities that arenot available in the base first module or existing modules within thebase first module. In one embodiment, the systems, apparatuses, andprocesses extend the functionality of a nucleic acid diagnostic firstmodule by supporting PCR assay processing and analysis capabilities inaddition to isothermal amplification processing and analysiscapabilities. A second module is operatively coupled to the base firstmodule to extend the overall system capabilities of the diagnosticsystem. Providing this extension module imparts sample-to-answercapabilities for a single automated instrument that, when incorporated,will be capable of automatically performing both thermal cycling andisothermal amplification assays, and which may incorporate end-point andreal-time formats using chemiluminescent and/or fluorescent labels.

In some embodiments, a diagnostic system can be configured to perform afirst nucleic acid amplification reaction and a second nucleic acidamplification reaction different than the first nucleic acidamplification reaction. The diagnostic system comprises at least onebulk reagent container compartment configured to store at least a firstbulk reagent container comprising a first bulk reagent for performing asample preparation process, and a second bulk reagent containercomprising a second bulk reagent for performing the first nucleic acidamplification reaction. The at least one bulk reagent containercompartment is further configured to store a unit-dose reagentcompartment configured to store at least one unit-dose reagent packcomprising a plurality of unit-dose reagents for performing the secondnucleic acid amplification reaction. The diagnostic system is configuredto perform the sample preparation process using the first bulk reagenton a first subset of the plurality of samples provided to the diagnosticsystem. The diagnostic system is also configured to perform the firstnucleic acid amplification reaction using a second bulk reagent on thefirst subset of the plurality of samples. And the diagnostic system isconfigured to perform the second nucleic acid amplification reactionusing the plurality of unit-dose reagents on a second subset of theplurality of samples.

In some embodiments, an automated method for analyzing a plurality ofsamples comprises performing a first assay on a first sample subset ofthe plurality of samples. The first assay comprises a first reactionthat uses a first unit-dose reagent. The method also comprisesperforming a second assay on a second sample subset of the plurality ofsamples. The second assay comprises a second reaction that uses at leastone of (a) a second unit-dose reagent different than the first unit-dosereagent and (b) a first bulk reagent. Performing the first assay andperforming the second assay occur within a same diagnostic system thatstores the first unit-dose reagent and at least one of the secondunit-dose reagent and the first bulk reagent.

In one exemplary embodiment, the base first module comprises a dualformat molecular diagnostic instrument designed to run specifictarget-amplified assays, utilizing chemiluminescence and fluorescencedetection technologies for both qualitative and real-time quantitativeassays. With the addition of the second module, additional automatedassays, such as PCR assays, can be run (intermixed) with assaysperformed by the base first module and achieve similar throughput thatis achieved by the base first module.

In one exemplary embodiment, the second module comprises a thermalcycler with real-time fluorescence detection capabilities, a reagentpack storage bay that allows for loading and cooled storage of newreagent packs containing reagents (e.g., PCR reagents), additionaldisposable pipette tip trays, PCR- and assay-specific reagents, and oneor more pipettor systems to perform the assay steps needed for the PCRor other reaction and/or receptacle transport. The second module mayrely on the base first module for sample input, sample preparation,target capture, and other processing steps, such as the addition ofelution for subsequent PCR assays, and thus the second module furtherleverages those capabilities of the base first module and supportsadditional processing and detection capabilities without requiring thatthe sample input and preparation functionality be built into the secondmodule.

Aspects of the disclosure are embodied in a second module for enhancingthe capabilities of a first module configured to process substanceswithin each of a plurality of receptacles and including a firstsubstance transfer device configured to dispense substances into eachreceptacle and a receptacle transfer device configured to movereceptacles within the first module. The second module is configured tobe coupled to or decoupled from the first module and comprises acontainer transport configured to transport at least one container froma location within the second module to a location within the firstmodule that is accessible to the first substance transfer device totransfer substance from the container to a receptacle within the firstmodule, a receptacle distribution module configured to receive areceptacle from the receptacle transfer device of the first module,transfer the receptacle into the second module, and move the receptaclebetween different locations within the first module, and a secondsubstance transfer device configured to dispense substances into orremove substances from the receptacle within the second module.

According to some aspects of the disclosure, the receptacle distributionmodule comprises a receptacle distributor configured to move areceptacle onto the receptacle distributor at a first location on thesecond module, carry the receptacle from the first location to a secondlocation on the second module that is different from the first location,and move the receptacle off the receptacle distributor at the secondlocation on the second module. A receptacle handoff device can beconfigured to receive a receptacle from the receptacle transfer deviceof the first module and to reposition the receptacle to present thereceptacle to the receptacle distributor to be moved by the receptacledistributor from the receptacle handoff device onto the receptacledistributor.

According to some aspects of the disclosure, the receptacle distributoris configured to rotate about an axis of rotation to move a receptaclecarried thereby in an arced path between locations within the secondmodule. Other configurations for moving a receptacle between locationswithin the second module are contemplated. Therefore, the disclosure isnot limited to receptacle distributors that rotate about an axis ofrotation.

According to some aspects of the disclosure, the second module furthercomprises receptacle storage stations for holding one or morereceptacles transferred from the first module to the second module,wherein the receptacle storage stations are arranged in a configurationcorresponding to the arced path of the receptacle distributor.

According to some aspects of the disclosure, the receptacle distributoris configured to move vertically a receptacle carried thereby betweendifferent vertically-disposed locations within the second module.

According to some aspects of the disclosure, the receptacle handoffdevice is configured to rotate between a first position for receiving areceptacle from the receptacle transfer device of the first module and asecond position for presenting the receptacle to the receptacledistributor.

According to some aspects of the disclosure, the second module furthercomprises a container compartment, configured to hold one or more fluidcontainers. In certain embodiments, the container compartment can be acontainer drawer configured to be moved between an open position and aclosed position and to, when moved to the closed position, place atleast one fluid container into an operative position with respect to thecontainer transport so that the container can be transported by thecontainer transport from the container compartment into the firstmodule. In an alternate embodiment, the container compartment cancomprise a door with a sliding tray that is configured to be movedbetween an open position and a closed position and to, when moved to theclosed position, place at least one fluid container into an operativeposition with respect to the container transport so that the containercan be transported by the container transport from the containercompartment into the first module.

According to some aspects of the disclosure, the second module furthercomprises a container carriage configured to carry one or morecontainers and to be movable with the container compartment and furtherconfigured to be engaged by the container transport when the containercompartment is in the closed position such that the container transportis operable to move the container carriage and the one or morecontainers carried thereby from the container compartment into the firstmodule.

According to some aspects of the disclosure, the second module furthercomprises a carriage transport and a carriage lock. The carriagetransport is moveable with the container receptacle and configured tocarry the container carriage between a first position when the containerreceptacle is in the open position and a second position when thecontainer receptacle is in the closed position. The carriage lock isconfigured to lock the container carriage to the carriage transport whenthe carriage transport is in the first position and to release thecontainer from the carriage transport when the carriage transport is inthe second position to permit the container carriage to be removed fromthe carriage transport by the container transport.

According to some aspects of the disclosure, the container transportcomprises a track extending from the container compartment into thefirst module, a carriage hook configured to engage the containercarriage when the container compartment is in the closed position, and amotorized carriage hook drive system configured to move carriage hookalong the carriage track.

According to some aspects of the disclosure, the motorized carriage hookdrive system comprises a motor and a belt driven by the motor andcoupled to the carriage hook.

According to some aspects of the disclosure, the processing apparatusfurther comprises one or more position sensors disposed at one or morelocations along the track to detect a position of the carriage on thetrack.

According to some aspects of the disclosure, the second module furthercomprises a reagent pack changer comprising a pack input device and apack storage compartment. The pack input device is configured to enablean operator to place a reagent pack containing at least one reagent intothe second module or remove a reagent pack from the second module. Thepack storage compartment is configured to hold a plurality of reagentpacks until a reagent pack is needed for processing within the secondmodule. The receptacle distribution module is further configured to movea reagent pack between the pack input device and the pack storagecompartment.

According to some aspects of the disclosure, the second module furthercomprises one or more reagent pack loading stations, each configured tohold a reagent pack in a manner that permits the second substancetransfer device to transfer a substance to or from the reagent pack.Therefore, in some embodiments, the reagent pack loading station isconfigured to change the orientation of the reagent pack from an initialloaded position to a position aligned with the second substance transferdevice.

According to some aspects of the disclosure, the second module furthercomprises a charged field generator operatively associated with at leastone of the pack input device, the pack storage compartment, and thereagent pack loading stations and configured to generate electrostaticforces to position and hold a reagent present in a reagent pack held inthe pack input device or pack storage compartment. In related aspectsthe charged field generator is situated below at least one of the packinput device, the pack storage compartment, and the reagent pack loadingstations such that electromagnetic forces are applied to, or adjacentto, the bottom of one or more wells of a reagent pack, when present.

According to some aspects of the disclosure, wherein the pack inputdevice comprises a reagent pack carousel that is rotatable about an axisof rotation, wherein the pack carousel includes a plurality of reagentpack stations, each configured to hold a reagent pack, disposed aroundthe axis of rotation.

According to some aspects of the disclosure, the pack carousel isdisposed in a compartment, such as a drawer, that is movable between anopen position providing access to the pack carousel and a closedposition closing off access to the pack carousel. The pack carousel canalso be accessed through an access panel revealing a slidable tray onwhich is mounted the pack carousel.

According to some aspects of the disclosure, the second module furthercomprises a code reader operatively disposed with respect to the packinput device and configured to read a machine readable code on eachreagent pack carried in the pack input device. In some embodiments, thecode reader reads the machine readable code on a respective reagent packin close proximity to the code reader.

According to some aspects of the disclosure, the second module furthercomprises a pack storage carousel disposed within the pack storagecompartment. The pack storage carousel is rotatable about an axis ofrotation and includes a plurality of reagent pack stations, eachconfigured to hold a reagent pack, disposed around the axis of rotation.

According to some aspects of the disclosure, the reagent pack stationsof the pack storage carrousel are disposed on more than one level of thesecond module.

According to some aspects of the disclosure, the second module furtherincludes a cooling system for maintaining the storage compartment at alower than ambient temperature.

According to some aspects of the disclosure, the second substancetransfer device comprises a robotic pipettor having a pipettor probe,and the second module further comprises one or more disposable tipcompartments configured to hold a plurality of disposable tipsconfigured to be placed on the pipettor probe of the robotic pipettor.

According to some aspects of the disclosure, the second module furthercomprises a cap/vial tray configured to hold a plurality of processingvials and/or associated caps. Each cap is configured to be coupled to anassociated vial to close the associated vial. The vials are accessibleby the robotic pipettor to dispense processing material into the vials,and the associated caps are accessible by the robotic pipettor to moveeach cap into an associated vial to form a cap/vial assembly. Therobotic pipettor is configured to move the cap/vial assembly from thecap/vial tray to another location on the second module.

According to some aspects of the disclosure, the second module furthercomprises a centrifuge, wherein the robotic pipettor is configured tomove a cap/vial assembly from the cap/vial tray to the centrifuge.

According to some aspects of the disclosure, the second module furthercomprises a thermal cycler configured to hold a plurality of cap/vialassemblies and to subject the contents of the plurality of cap/vialassemblies to cyclically varying temperatures and a robotic vialtransfer arm configured to move a cap/vial assembly from the centrifugeto the thermal cycler.

According to some aspects of the disclosure, the second module furthercomprises one or more magnetic receptacle holding slots configured tohold a receptacle transferred from the first module to the secondmodule. Each magnetic receptacle holding slot comprises a magnet and isconfigured to draw magnetic particles contained within the receptacle toa wall of the receptacle and out of solution within the fluid contentsof the receptacle.

According to some aspects of the disclosure, the first module and thesecond module are configured to conduct nucleic acid amplificationreactions.

According to some aspects of the disclosure, the nucleic acidamplification reactions conducted in the first module and the secondmodule are different types of amplification reactions.

According to some aspects of the disclosure, the nucleic acidamplification reaction conducted in the first module comprises aqualitatively monitored reaction and the nucleic acid amplificationreaction conducted in the second module comprises a quantitativelymonitored reaction.

According to some aspects of the disclosure, the nucleic acidamplification reaction conducted in the second module comprises areaction monitored in real-time.

According to some aspects of the disclosure, wherein the nucleic acidamplification reaction conducted in the first module is an isothermalreaction, and the nucleic acid amplification reaction conducted in thesecond module comprises the use of a polymerase chain reaction.

Aspects of the disclosure are further embodied in an automated systemcapable of performing multiple molecular assays on a single sample. Thesystem comprises a sample input portal configured to accept samplescontained in one or more receptacles, a sample preparation moduleconfigured to prepare a sample provided to the sample input portal for anucleic acid amplification reaction, a first module configured toconduct an isothermal nucleic acid amplification assay with the sample,a second module configured to conduct a nucleic acid amplification assayinvolving temperature cycling with the sample, and a transport mechanismconfigured to effect automated transport of one or more receptaclescontaining the sample between the sample input portal, the samplepreparation module, the first module, and the second module.

According to some aspects of the disclosure, the automated systemfurther comprises a substance transfer device configured to access thesample when present in the sample second module, the first module, orthe second module.

According to some aspects of the disclosure, the system furthercomprises a reagent storage compartment configured to hold a pluralityof reagent containers, wherein the reagent storage compartment is heldat a temperature below ambient temperature.

According to some aspects of the disclosure, the system furthercomprises a reagent container transport mechanism configured totransport one or more reagent containers between the reagent storagecompartment and a separate location within the second module.

According to some aspects of the disclosure, the reagent containertransport mechanism is configured to transport the reagent containerswithin the second module and to transport the receptacles within thesecond module.

Some aspects of the disclosure are embodied in a method for improvedthermal cycling of low volume nucleic acid amplification reactionmixtures. The method comprises combining a fluid sample together withone or more amplification reaction reagents in a reaction receptacleusing an automated pipettor, transporting the reaction receptacle to acentrifuge using the automated pipettor, centrifuging the fluid contentsof the reaction receptacle, automatically removing the reactionreceptacle from the centrifuge after centrifugation and placing thereaction receptacle in a thermal cycler, and subjecting the fluidcontents of the reaction receptacle to one or more temperature cycleswithin the thermal cycler.

According to some aspects of the disclosure, the reaction receptacle isremoved from the centrifuge and transported to the thermal cycler usingthe vial transfer arm.

According to some aspects of the disclosure, the reaction receptacle isplaced in the centrifuge at a first location, and the reactionreceptacle is removed from the centrifuge at a second, differentlocation.

According to some aspects of the disclosure, the method furthercomprises a second automated pipettor, and the second automated pipettorautomatically removes the reaction receptacle from the centrifuge aftercentrifugation and places the reaction receptacle in the thermal cycler.

According to some aspects of the disclosure, the receptacle is sealed bya cap before transporting the sealed receptacle to the centrifuge.

According to some aspects of the disclosure, the automated pipettortransports the cap to the receptacle and seals the receptacle bycoupling the cap to the receptacle.

Some aspects of the disclosure are embodied in an improved method ofpreparing multiple different nucleic acid reaction mixtures within theworkflow of an automated molecular instrument. The method comprisesproviding two or more reaction receptacles, providing two or more unitdose reagent containers, each unit dose reagent container correspondingto a respective reaction receptacle, and each unit dose reagentcontainer containing a nucleic acid amplification reagent that isspecific for one or more target nucleic acids, providing a receptaclecontaining a first bulk reagent, and combining at least a portion of thesample with at least a portion of the unit dose reagent and at least aportion of the bulk reagent in each of the two or more reactionreceptacles. After combination, each reaction receptacle contains adifferent sample, a different unit dose reagent, and the same first bulkreagent.

According to further aspects of the disclosure, the method furthercomprises a receptacle containing a second bulk reagent, wherein thesecond bulk reagent is dispensed into each of the two or more unit dosereagent containers before combining at least a portion of the samplewith at least a portion of the unit dose reagent and at least a portionof the bulk reagent in each of the two or more reaction receptacles.

According to some aspects of the disclosure, the second bulk reagentcomprises a reconstitution reagent.

According to some aspects of the disclosure, the method furthercomprises transporting each of the two or more reaction receptacles to aheater, such as a heated incubator or a heating plate, to conduct anucleic acid amplification assay.

Other features and characteristics of the present disclosure, as well asthe methods of operation, functions of related elements of structure andthe combination of parts, and economies of manufacture, will become moreapparent upon consideration of the following description and theappended claims with reference to the accompanying drawings, all ofwhich form a part of this specification, wherein like reference numeralsdesignate corresponding parts in the various FIGS.

DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are incorporated herein and form partof the specification, illustrate various, non-limiting embodiments ofthe present disclosure. In the drawings, common reference numbersindicate identical or functionally similar elements.

FIG. 1 is a perspective view of a diagnostic system comprising a firstmodule and a second module according to an embodiment.

FIG. 2 is a perspective view of a multiple receptacle device (“MRD”)according to an embodiment.

FIG. 3 is a partial bottom view of the MRD of FIG. 2.

FIG. 4 is a top plan view of a first module of a diagnostic systemaccording to an embodiment.

FIG. 5 is an exploded, top plan view of the first module and the secondmodule according to an embodiment.

FIG. 6 is a top plan view of an amplification processing deck of thesecond module according to an embodiment.

FIG. 7 is a partial, front perspective view of the second module with abulk reagent container compartment in an open position according to anembodiment.

FIG. 8 is a partial, top plan view of the second module and first moduleshowing the bulk reagent container compartment in a closed positionaccording to an embodiment.

FIG. 9 is a top perspective view of the bulk reagent containercompartment and bulk reagent container transport of the second module,with the bulk reagent container compartment in an open positionaccording to an embodiment.

FIG. 10 is a top perspective view of the bulk reagent containercompartment and bulk reagent container transport of the second module,with the bulk reagent container compartment in a closed position andelution containers transported to an end of the bulk reagent containertransport according to an embodiment.

FIG. 11 is a partial cross-sectional view of bulk reagent containercompartment, with the bulk reagent container compartment in an openposition according to an embodiment.

FIG. 12 is a partial cross-sectional view of bulk reagent containercompartment and the bulk reagent container transport, with the bulkreagent container compartment in a closed position according to anembodiment.

FIG. 13 is a partial end view of bulk reagent container compartment,with the bulk reagent container compartment in a closed positionaccording to an embodiment.

FIG. 14 is a top perspective view of a receptacle processing deck of thesecond module according to an embodiment.

FIG. 15 is a partial, front perspective view of the second module with acarousel compartment of a reagent pack changer in an open positionaccording to an embodiment.

FIG. 16 is a partial, top perspective view of the pack carouselcompartment according to an embodiment.

FIG. 17 is a partial, side perspective view of the pack carouselcompartment according to an embodiment.

FIG. 18 is a cross-sectional, rear perspective view of an alternativeembodiment of a reagent pack changer and a reagent pack storagecompartment.

FIG. 19 is a top perspective view of a reagent pack embodying aspects ofthe present disclosure according to an embodiment.

FIG. 20 is a top perspective, cross-sectional view of a reagent packalong the line XX-XX in FIG. 19 according to an embodiment.

FIG. 21 is a perspective view of a robotic pipettor of the second moduleaccording to an embodiment.

FIG. 22 is a perspective view of a substance transfer pipettor of therobotic pipettor according to an embodiment.

FIG. 23 is an exploded, perspective view of a processing vial, aprocessing vial cap, and a pipettor probe according to an embodiment.

FIG. 24 is a transverse cross-section of the processing vial and theprocessing vial cap disposed within a processing vial well and a capwell, respectively, of a processing cap/vial compartment tray accordingto an embodiment.

FIG. 25 is a transverse cross-section of the processing vial cap removedfrom the cap well and inserted into the processing vial with theprocessing vial disposed within the processing vial well according to anembodiment.

FIG. 26 is an exploded, perspective view of an alternative embodiment ofa processing vial, a processing vial cap, and a pipettor probe.

FIG. 27 is a top perspective view of an embodiment of a receptacledistribution module of the second module.

FIG. 28 is a bottom perspective view of the receptacle distributionmodule according to an embodiment.

FIG. 29 is a perspective view of an embodiment of a distributor head ofa rotary distributor of the receptacle distribution module with areceptacle hook in a retracted position.

FIG. 30 is a perspective view of the distributor head with thereceptacle hook in an extended position according to an embodiment.

FIG. 31 is an opposite side perspective view of the distributor headaccording to an embodiment.

FIG. 32 is a transverse cross-section of the rotary distributor with areagent pack disposed therein according to an embodiment.

FIG. 33 is a transverse cross-section of the rotary distributor with anMRD disposed therein according to an embodiment.

FIG. 34 is a top front perspective view of an embodiment of adistributor moving system of the receptacle distribution module.

FIG. 35 is a top rear perspective view of the distributor moving system.

FIG. 36 is a top plan view of an embodiment of magnetic elution slotsand reagent pack loading stations of the second module.

FIG. 37 is a front end perspective view of the magnetic elution slotsand reagent pack loading stations according to an embodiment.

FIG. 38 is a back end perspective view of the magnetic elution slots andreagent pack loading stations according to an embodiment.

FIGS. 39 and 40 are perspective views of an embodiment of an MRD handoffdevice of the second module.

FIG. 41 is a flowchart illustrating the steps of a sample eluatepreparation process according to an embodiment.

FIG. 42 is a flowchart illustrating the steps of a reaction mixturepreparation process according to an embodiment.

FIG. 43 is a flowchart illustrating the steps of a process forperforming an automated nucleic acid amplification reaction, such asPCR, according to an embodiment.

FIG. 44 is a flowchart illustrating a method of using diagnostic systemaccording to one such embodiment.

FIGS. 45-48 show a receptacle of the present disclosure. FIG. 45 is aside view of the receptacle. FIG. 46 is a cross-sectional view of thereceptacle taken along a vertical axis of view shown in FIG. 45. FIG. 47top view of the receptacle. FIG. 48 is a perspective view of thereceptacle.

FIGS. 49-54 show a cap of the present disclosure. FIG. 49 is a side viewof the cap. FIG. 50 is a cross-sectional view of the cap taken along avertical axis of the view shown in FIG. 49. FIG. 51 is a top view of thecap. FIG. 52 is a bottom view of the cap. FIGS. 53 and 54 are top andbottom perspective views of the cap.

FIG. 55 is a cross-sectional view of the cap secured to the receptacle,and insertion of an automated pipettor into the open end of the cap.

FIG. 56 shows an apparatus of the present disclosure.

FIG. 57 shows an apparatus of the present disclosure mounted in ahousing.

FIGS. 58-60 show a receptacle holder of the present disclosure.

FIGS. 61 and 62 show a receptacle holder slidably mounted to a support.The support is mounted in thermal communication with a heat sink (FIG.61). A cross-brace may be mounted to the support to exert a force onto afront surface the receptacle holder (FIG. 62).

FIGS. 63-67 show exemplary covers and stripper plates disposed withinthe apparatus of the present disclosure.

FIG. 68 show an exemplary embodiment of an apparatus of the presentdisclosure.

FIGS. 69-71 show a modified pipettor for use as a receptacle transportmechanism within a system of the present disclosure.

FIGS. 72-74 show an embodiment providing movement of the optical fibersof the apparatus of the present disclosure and the forces associatedtherewith prior to and after seating receptacles within the receptaclewells of a receptacle holder.

FIG. 75 shows an apparatus in optical communication with an excitationsignal source and/or an emission signal detector within a housing of aninstrument for performing a biochemical assay.

FIGS. 76 and 77 are flow charts showing exemplary steps involved in amethod for establishing optical communication between a receptacle andan excitation signal source and/or an emission signal detector within ahousing of the apparatus while allowing maximal contact between thesurface of the receptacle well and the receptacle.

FIG. 78 is a perspective view of a signal detection module embodyingaspects of the present disclosure.

FIG. 79 is a perspective view of a signal detector head.

FIG. 80 is a transverse cross-section of the signal detector head alongthe line XIII-XIII in FIG. 79.

FIG. 81 is a schematic view of an embodiment of an exemplary opticalpath within a signal detector.

FIG. 82 is a schematic view of the signal detection module embodyingaspects of the present disclosure and a power and data control systemincorporated therewith.

DETAILED DESCRIPTION

Unless defined otherwise, all terms of art, notations and otherscientific terms or terminology used herein have the same meaning as iscommonly understood by one of ordinary skill in the art to which thisdisclosure belongs. Many of the techniques and procedures described orreferenced herein are well understood and commonly employed usingconventional methodology by those skilled in the art. As appropriate,procedures involving the use of commercially available kits and reagentsare generally carried out in accordance with manufacturer definedprotocols and/or parameters unless otherwise noted. All patents,applications, published applications, and other publications referred toherein are incorporated by reference in their entirety. If a definitionset forth in this section is contrary to or otherwise inconsistent witha definition set forth in the patents, applications, publishedapplications, and other publications that are herein incorporated byreference, the definition set forth in this section prevails over thedefinition that is incorporated herein by reference.

References in the specification to “one embodiment,” “an embodiment,” a“further embodiment,” “an example embodiment,” “some aspects,” “afurther aspect,” “aspects,” etc., indicate that the embodiment describedmay include a particular feature, structure, or characteristic, butevery embodiment may not necessarily include the particular feature,structure, or characteristic. Moreover, such phrases are not necessarilyreferring to the same embodiment. Further, when a particular feature,structure, or characteristic is described in connection with anembodiment, such feature, structure, or characteristic is also adescription in connection with other embodiments whether or notexplicitly described.

As used herein, “a” or “an” means “at least one” or “one or more.”

As used herein, “sample” refers to any substance suspected of containinga virus or organism of interest or, alternatively, nucleic acid derivedfrom the virus or organism of interest, or any substance suspected tohave a nucleic acid of interest, such as a nucleic acid suspected ofhaving genetic abnormalities or mutations. The substance may be, forexample, an unprocessed clinical specimen, such as a blood orgenitourinary tract specimen, a buffered medium containing the specimen,a medium containing the specimen and lytic agents for releasing nucleicacid belonging to the virus or organism, or a medium containing nucleicacid derived from the virus or organism which has been isolated and/orpurified in a reaction receptacle or on a reaction material or device.For this reason, the term “sample” will be understood to mean a specimenin its raw form or to any stage of processing to release, isolate andpurify nucleic acid derived from the virus or organism. Thus, referencesto a “sample” may refer to a substance suspected of containing nucleicacid derived from a virus or organism at different stages of processingand is not limited to the initial form of the substance.

This description may use relative spatial and/or orientation terms indescribing the position and/or orientation of a component, apparatus,location, feature, or a portion thereof. Unless specifically stated, orotherwise dictated by the context of the description, such terms,including, without limitation, top, bottom, above, below, under, on topof, upper, lower, left of, right of, inside, outside, inner, outer,proximal, distal, in front of, behind, next to, adjacent, between,horizontal, vertical, diagonal, longitudinal, transverse, etc., are usedfor convenience in referring to such component, apparatus, location,feature, or a portion thereof in the drawings and are not intended to belimiting.

The section headings used in the present application are merely intendedto orient the reader to various aspects of the disclosed system. Thesection headings are not intended to limit the disclosed and claimedinventions. Similarly, the section headings are not intended to suggestthat materials, features, aspects, methods, or procedures described inone section do not apply in another section. Therefore, descriptions ofmaterials, features, aspects, methods or procedures described in onesection are intended to apply to other sections.

Nucleic Acid Diagnostic Assays

Aspects of the present disclosure involve diagnostic systems and methodsthat can be used in conjunction with nucleic acid diagnostic assays,including “real-time” amplification assays and “end-point” amplificationassays.

Real-time amplification assays can be used to determine the presence andamount of a target nucleic acid in a sample which, by way of example, isderived from a pathogenic organism (e.g., bacterium, fungus, orprotozoan) or virus. Thus, real-time amplification assays are oftenreferred to as quantitative assays. By determining the quantity of atarget nucleic acid in a sample, a practitioner can approximate theamount or load of the organism or virus in the sample. In oneapplication, a real-time amplification assay may be used to screen bloodor blood products intended for transfusion for blood borne pathogens,such as hepatitis C virus (HCV) and human immunodeficiency virus (HIV).In another application, a real-time assay may be used to monitor theefficacy of a therapeutic regimen in a patient infected with apathogenic organism or virus, or that is afflicted with a diseasecharacterized by aberrant or mutant gene expression. Real-timeamplification assays may also be used for diagnostic purposes, as wellas in gene expression determinations. Exemplary systems and methods forperforming real-time amplification assays are disclosed by Macioszek etal. in U.S. Pat. No. 7,897,337.

In addition to implementation of embodiments of the disclosure inconjunction with real-time amplification assays, embodiments of thedisclosure may also be implemented in conjunction with end-pointamplification assays. In end-point amplification assays, the presence ofamplification products containing the target sequence or its complementis determined at the conclusion of an amplification procedure. Thus,end-point amplification assays are often referred to as qualitativeassays in that such assays do not indicate the amount of a targetanalyte present, but provide a qualitative indication regarding thepresence or absence of the target analyte. Exemplary systems and methodsfor end-point detection are disclosed by Ammann et al. in U.S. Pat. No.6,335,166. The determination may occur in a detection station that isintegral with or at an external location relative to the incubator(s) inwhich the amplification reactions occur. In contrast, in “real-time”amplification assays, the amount of amplification products containingthe target sequence or its complement is determined during anamplification procedure. In a real-time amplification assay, theconcentration of a target nucleic acid can be determined using dataacquired by making periodic measurements of signals that are a functionof the amount of amplification product in the sample containing thetarget sequence or its complement, and calculating the rate at which thetarget sequence is being amplified from the acquired data. An example ofsuch a real-time amplification assay is described by Light II et al. inU.S. Pat. No. 8,615,368.

In an exemplary real-time amplification assay, the interacting labelsinclude a fluorescent moiety, or other emission moiety, and a quenchermoiety, such as, for example, 4-(4-dimethylaminophenylazo) benzoic acid(DABCYL). The fluorescent moiety emits light energy (i.e., fluoresces)at a specific emission wavelength when excited by light energy at anappropriate excitation wavelength. When the fluorescent moiety and thequencher moiety are held in close proximity, light energy emitted by thefluorescent moiety is absorbed by the quencher moiety. But when a probehybridizes to a nucleic acid present in the sample, the fluorescent andquencher moieties are separated from each other and light energy emittedby the fluorescent moiety can be detected. Fluorescent moieties havingdifferent and distinguishable excitation and emission wavelengths areoften combined with different probes. The different probes can be addedto a sample, and the presence and amount of target nucleic acidsassociated with each probe can be determined by alternately exposing thesample to light energy at different excitation wavelengths and measuringthe light emission from the sample at the different wavelengthscorresponding to the different fluorescent moieties. In anotherembodiment, different fluorescent moieties having the same excitationwavelength, but different and distinguishable emission wavelengths arecombined with different probes. The presence and amount of targetnucleic acids associated with each probe can be determined by exposingthe sample to a specific wavelength light energy and the light emissionfrom the sample at the different wavelengths corresponding to thedifferent fluorescent moieties is measured.

A variety of different labeled probes and probing mechanisms are knownin the art, including those where the probe does not hybridize to thetarget sequence. See, e.g., Brow et al. in U.S. Pat. No. 5,846,717 andChun et al. in U.S. Patent Application Publication No. 2013/0109588.Some embodiments of the present disclosure operate regardless of theparticular labeling scheme utilized, provided the moiety to be detectedcan be excited by a particular wavelength of light and emits adistinguishable emission spectra.

Where a nucleic acid amplification reaction is used to increase theamount of target sequence and/or its complement present in a samplebefore detection, it is desirable to include a “control” to ensure thatamplification has taken place. See, for example, the amplificationcontrols described by Wang in U.S. Pat. No. 5,476,774. Such a controlcan be a known nucleic acid sequence that is unrelated to thesequence(s) of interest. A probe (i.e., a control probe) havingspecificity for the control sequence and having a unique fluorescent dye(i.e., the control dye) and quencher combination is added to the sample,along with one or more amplification reagents needed to amplify thecontrol sequence, as well as the target sequence(s). After exposing thesample to appropriate amplification conditions, the sample isalternately exposed to light energy at different excitation wavelengths(including the excitation wavelength for the control dye) and emissionlight is detected. Detection of emission light of a wavelengthcorresponding to the control dye confirms that the amplification wassuccessful (i.e., the control sequence was indeed amplified), and thus,any failure to detect emission light corresponding to the probe(s) ofthe target sequence(s) is not likely due to a failed amplification.Conversely, failure to detect emission light from the control dye may beindicative of a failed amplification, thus calling into question theresults from that assay. Alternatively, failure to detect emission lightmay be due to failure or deteriorated mechanical and/or electricalperformance of an instrument for detecting the emission light.

In some embodiments, the assays performed in accordance with thedescription herein capture, amplify, and detect nucleic acids fromtarget organisms in patient samples employing technologies, such astarget capture, reverse transcription, and real-time polymerase chainreaction. The combination of reverse transcription and PCR isabbreviated “RT-PCR.” The following is a generalized assay processingdescription of the different technologies that may be implemented inaccordance with aspects of the disclosure.

The target capture process isolates nucleic acid of the target (e.g.,virus, bacterium, fungus, protozoan, mammalian cells, etc.) and purifiesnucleic acid for amplification. The target organism, which can be in avariety of biological matrices from urine to blood, can be lysed bytarget capture reagents (“TCR”), whereby the nucleic acid is released.In one approach, capture oligonucleotide probes hybridize to a targetnucleic acid. The capture probe/target nucleic acid complexes attach tomagnetic particles in the TCR through nucleic acid hybridization.Exemplary disclosures for performing these methods are provided by U.S.Pat. Nos. 6,140,678, 5,234,809, 5,693,785, and 5,973,138, and EP PatentNo. 0 389 063. The magnetic particles are pulled to the side of acontainer and isolated by a magnet, and potential inhibitory substancesare washed away (multiple wash cycles may be performed) to therebyprovide a target nucleic acid. Hogan et al. provide an exemplarydisclosure of this protocol in U.S. Pat. No. 7,172,863. See alsoInternational Publication No. WO 2003/097808 by Fort et al. If thetarget capture process is specific for the target nucleic acid, then itis the target nucleic acid that will primarily remain after thepurification step. As a result, target capture enables the enrichment ofa variety of sample types and significantly reduces the inhibition rateand can increase assay sensitivity. Exemplary methods of target nucleicacid capture are disclosed by, for example, Boom et al. in U.S. Pat. No.5,234,864, Hawkins in U.S. Pat. No. 5,705,628, Collins et al. in U.S.Pat. No. 5,750,338, and Weisburg et al. in U.S. Pat. No. 6,534,273.

After completing the target capture process, the magnetic particles onwhich the target nucleic acid is immobilized are re-suspended, forexample, with 20-60 μL of a wash solution comprising a low salt bufferor water. This will de-hybridize the target nucleic acid from themagnetic particles and, in the presence of a strong magnet, allow 5-50μL of purified nucleic acid to be recovered as input into theamplification process.

Reverse transcription and PCR can be optimized to run in a singlereceptacle using common reagents as a one-step process. This methodprovides a sensitive means to detect low-abundance RNAs, and, althoughthe method is not necessarily quantitative, specific controls can beincluded in the experiment if quantitative results are desired. (Areverse-transcription step is not required if the target nucleic acid isDNA.) In an exemplary implementation, before performing the real-timePCR reaction, RNAs are incubated with a retroviral enzyme (reversetranscriptase) under oil at 42° C. for approximately 30 minutes. Thisprocess creates a single-stranded DNA copy of the RNA target sequence.If the goal is to copy all RNAs present in the source material into DNA,non-specific primers or primer sets are used. In the case of mRNA, whichhas a polyadenylated (poly A) tail, an oligo dT primer can be used.Alternatively, a collection of randomized hexanucleotide primers can beused to ensure an primer will be present that is complementary to eachof the messages. If only one RNA target is sought, a sequence-specificprimer complementary to the 3′ end of the desired amplification productis used. RNase H is used to degrade the RNA molecule contained in thehybrid RNA-DNA duplex, so that the DNA strand is available to directsecond-strand synthesis. Single-stranded DNA thus generated can serve asthe template for PCR using sequence-specific primers to amplify theregion of interest.

The polymerase is inactive at low temperatures and can be heat activatedat 95° C. for several minutes (for example, approximately 10 minutes)before beginning PCR. Both reactions occur inside a thermal cycler(i.e., a module configured to expose the contents of the receptacle totemperatures that are cycled between two or more differenttemperatures), but real-time PCR requires accurate/rapid thermal cyclingbetween denaturation (˜95° C.), annealing (˜55° C.), and synthesis (˜72°C.) temperatures. Fluorescence monitoring occurs at one or many colorwavelengths—relating to one or many probes adapted to detect one or manytarget analytes—during each cycle or at another predetermined interval.PCR components may include, for example, the forward and reverse primersand a fluorogenic probe containing a reporter fluorescent dye on the 5′end and a quencher dye on the 3′ end. (See, e.g., Holland et al., Proc.Natl. Acad. Sci. USA, 88(16):7276-7280 (1991).) During PCR, nucleic acidprimers hybridize to opposite strands of the target nucleic acid and areoriented with their 3′ ends facing each other so that synthesis by anucleic acid polymerization enzyme, such as a DNA polymerase, extendsacross the segment of the nucleic acid between them. While the probe isintact, the proximity of the quencher dye to the reporter dye greatlyreduces the fluorescence emitted by the reporter dye. Duringamplification if the target nucleic acid is present, the fluorogenicprobe anneals downstream from one of the primer sites and is cleaved bythe 5′ nuclease activity of the polymerization enzyme during primerextension. The cleavage of the probe separates the reporter dye from thequencher dye, thus rendering detectable the reporter dye signal andremoving the probe from the target strand, allowing primer extension tocontinue to the end of the template strand.

One round of PCR synthesis will result in new strands of indeterminatelength which, like the parental strands, can hybridize to the primersupon denaturation and annealing. These products accumulatearithmetically with each subsequence cycle of denaturation, annealing toprimers, and synthesis. The second cycle of denaturation, annealing, andsynthesis produces two single-stranded products that together compose adiscrete double-stranded product which is exactly the length between theprimer ends. Each strand of this discrete product is complementary toone of the two primers and can therefore participate as a template insubsequent cycles. The amount of this product doubles with everysubsequent cycle of synthesis, denaturation and annealing. Thisaccumulates exponentially so that 30 cycles should result in a 2²⁸-fold(270 million-fold) amplification of the discrete product.

Multiple Receptacle Devices

FIG. 2 illustrates one embodiment of MRD 160 that comprises a pluralityof individual receptacles, or tubes, 162, preferably five. Thereceptacles 162 are formed to have open top ends and closed bottom ends(preferably in the form of cylindrical tubes), and are connected to oneanother by a connecting rib structure 164 which defines a downwardlyfacing shoulder extending longitudinally along either side of the MRD160.

Alternatively, the receptacle may be any container suitable for holdinga fluid or liquid, including, for example, a cuvette, vial, beaker, wellof a microtiter plate, test tube, and in some embodiments, a pipettetip. Unless explicitly stated or the context dictates otherwise,descriptions of an MRD or receptacle of an MRD are exemplary and shouldnot be construed as limiting of the scope of the disclosure, as aspectsof the disclosure are applicable to any suitable “receptacle.”

The MRD 160 in certain embodiments is formed from injection moldedpolypropylene, such as those sold by Montell Polyolefins, of Wilmington,Delaware, product number PD701NW or Huntsman, product number P5M6K-048.In an alternative embodiment, the receptacles 162 of the MRD arereleasably fixed with respect to each other by means such as, forexample, a sample tube rack or other holding structure.

An arcuate shield structure 169 can be provided at one end of the MRD160. An MRD manipulating structure 166 extends from the shield structure169. In certain embodiments, the manipulating structure 166 isconfigured to be engaged by an extendible and retractable hook of areceptacle distributor or a transport mechanism for moving the MRD 160between different components of a first module of a diagnostic system.An exemplary transport mechanism that is compatible with the MRD 160 isdisclosed by Ammann et al. in U.S. Pat. No. 6,335,166. The transportmechanism, in certain embodiments, engages the manipulating structure166 from the underside of the manipulating structure as shown with arrow60. In certain embodiments, the MRD manipulating structure 166 comprisesa laterally extending plate 168 extending from shield structure 169 witha vertically extending piece 167 on the opposite end of the plate 168. Agusset wall 165 can extend downwardly from lateral plate 168 betweenshield structure 169 and vertical piece 167.

As shown in FIG. 3, the shield structure 169 and vertical piece 167 havemutually facing convex surfaces. This, however, is just one way that theshield structure 169 and vertical piece 167 can be configured. The MRD160 may be engaged by a receptacle distributor, a transport mechanism,and other components, by moving an engaging member, such as anextendible and retractable hook, laterally (in the direction “A”) intothe space between the shield structure 169 and the vertical piece 167.The convex surfaces of the shield structure 169 and vertical piece 167provide for wider points of entry for an engaging member undergoing alateral relative motion into the space between the shield structure 169and the vertical piece 167. Of course, as the engaging member isrobotically controlled, it is understood that the convex surfaces aremerely a design choice of the present embodiment and that other shapedsurfaces are contemplated.

A label-receiving structure 174 having a flat label-receiving surface175 can be provided on an end of the MRD 160 opposite the shieldstructure 169 and MRD manipulating structure 166. Human and/ormachine-readable labels, such as scanable bar codes, can be placed onthe surface 175 to provide identifying and instructional information onthe MRD 160.

Further details regarding a representative MRD 160 are disclosed byHomer et al. in U.S. Pat. No. 6,086,827.

Diagnostic System

FIG. 1 illustrates a diagnostic system 10 according to an embodiment.Diagnostic system 10 can be configured to perform a plurality ofdifferent molecular assays on a plurality of samples. In someembodiments, diagnostic system 10 can be configured to perform differenttarget nucleic acid amplification reactions. For example, diagnosticsystem 10 can be configured to perform a first target nucleic acidamplification reaction on a first subset of a plurality of samples, andperform a second, different target nucleic acid amplification reactionon a second subset of the plurality of samples.

In some embodiments, diagnostic system 10 comprises a first module 100configured to perform at least one of the steps of a first targetnucleic acid amplification reaction, and a second module 400 configuredto perform at least one of the steps of a second target nucleic acidamplification.

In some embodiments, diagnostic system 10 is an integral, self-containedstructure—first module 100 cannot be selectively coupled to anddecoupled from second module 400.

In some embodiments, diagnostic system 10 is configured such that firstmodule 100 can be selectively and operatively coupled to second module400, and first module 100 can be selectively decoupled from secondmodule 400. In some embodiments, first module 100 can be selectivelycoupled to second module 400 using, for example, mechanical fasteners(for example, bolts or screws), clamps, any combination thereof, or anyother suitable attachment device. In some embodiments, suitable powerand/or data lines are provided between the second module 400 and thefirst module 100. For example, in embodiments in which first module 100can be selectively coupled to second module 400, second module 400 canextend the overall system capabilities of a diagnostic system includingonly first module 100 that was previously purchased by a customer.

The configurations and functions of first module 100 and second module400 according to various embodiments are described below.

First Module

A first module 100 in which embodiments of the present disclosure may beimplemented is shown schematically in plan view and designated byreference number 100 in FIG. 4. The first module 100 includes variousdevices configured to receive one or more reaction receptacles(described in more detail below), within each of which is performed oneor more steps of a multi-step nucleic acid test (NAT) designed to detecta virus or organism (e.g., bacterium, fungus, or protozoan). Firstmodule 100 can include receptacle-receiving components configured toreceive and hold one or more reaction receptacles and, in someinstances, to perform processes on the contents of the receptacles.Exemplary processes include, but are not limited to, adding substancessuch as sample fluid, reagents (e.g., target capture reagents,amplification reagents, buffers, oils, labels, probes, or any otherreagent) and/or removing substances from a reaction receptacle;agitating a receptacle to mix the contents thereof; maintaining and/oraltering the temperature of the contents of a reaction receptacle;heating or chilling the contents of a reaction receptacle; altering theconcentration of one or more components of the contents of a reactionreceptacle; separating or isolating constituent components of thecontents of a reaction receptacle; detecting an electromagnetic signalemission (e.g., light) from the contents of a reaction receptacle;deactivating or halting an on-going reaction; or any combination of twoor more of such processes.

In some embodiments, the first module 100 may include a receptacle inputdevice 102 that includes structure for receiving and holding one or moreempty reaction receptacles before the receptacles are used forperforming one or more process steps of a NAT. The receptacle inputdevice 102 may comprise a compartment, for example, a drawer or cabinet,that may be opened and loaded with a plurality of receptacles and mayinclude a receptacle feeding device for moving receptacles, for example,one or more at a time, into a receptacle pick-up position. In someembodiments, the receptacle pick-up position comprises a registered orknown position of the receptacle to facilitate removal of the receptacleby a receptacle distributor.

In some embodiments, the first module 100 may further include one ormore bulk reagent container compartments configured to store one or morebulk containers that hold bulk reagents or hold waste material. In someembodiments, the bulk reagents include fluids such as water, buffersolution, target capture reagents, nucleic acid amplification reagents.In some embodiments, the bulk reagent container compartments may beconfigured to maintain the contents of such containers at prescribedstorage temperatures and/or to agitate such containers to maintain thecontents of the containers in solution or suspension.

In some embodiments, first module 100 comprises a first bulk reagentcontainer compartment configured to store at least one bulk containerthat holds a nucleic acid amplification reagent, for example, a reagentfor performing TMA, and a separate second bulk reagent containercompartment configured to store at least one bulk container that holds asample preparation reagent, for example, a target capture reagent. Insome embodiments, first module 100 comprises a bulk reagent containercompartment that stores both a bulk container that holds a nucleic acidamplification reagent and a bulk container that holds a samplepreparation reagent, for example, a target capture reagent. In someembodiments, a bulk reagent container compartment that is configured tostore at least one bulk container can be a compartment that houses amixer, for example, an orbital mixer, that is configured to carry acontainer holding a sample preparation reagent, for example, a targetcapture reagent. In some embodiments, the one or more bulk containercompartments can comprise a holding structure for carrying and agitatingcontainers (e.g., containers of TCR with magnetically-responsive solidsupports). Buse et al. in U.S. Provisional Application No. 61/783,670,“Apparatus for Indexing and Agitating Fluid Containers,” filed Mar. 14,2013, which enjoys common ownership herewith, discloses an exemplaryholding structure. In some embodiments, one or more bulk containercompartments comprise a slidable tray that defines at least one recessconfigured to closely receive respective bulk containers.

In some embodiments, one or more of the bulk reagent containercompartments of first module 100 can be configured to store at least twocontainers containing sample preparation reagents, for example, targetcapture reagents. In some embodiments, each target capture reagent isspecific for a particular assay type (i.e., target nucleic acid), thetype of nucleic acid (e.g., RNA or DNA), and/or the sample type (e.g.,stool, urine, blood, etc.). For example, the target capture reagents cancomprise probes having a region specific for the target nucleic acid.See, e.g. Weisburg et al. in U.S. Pat. No. 6,534,273.

The first module 100 may further include a sample loading deviceconfigured to receive and hold containers, such as test tubes,containing samples. The first module 100 may also include one or moresubstance transfer devices for transferring fluids, for example, samplefluids, reagents, bulk fluids, waste fluids, etc., to and from reactionreceptacles and/or other containers. In some embodiments, the substancetransfer devices may comprise one or more robotic pipettors configuredfor controlled, automated movement and access to the reactionreceptacles, bulk containers holding reagents, and containers holdingsamples. In some embodiments, the substance transfer devices may alsoinclude fluid dispensers, for example, nozzles, disposed within otherdevices and connected by suitable fluid conduits to containers, forexample, bulk containers holding the reagents, and to pumps or otherdevices for causing fluid movement from the containers to thedispensers.

In some embodiments, the first module 100 may further include aplurality of load stations, such as load stations 104, 106, 108 depictedin FIG. 4, which are configured to receive racks and other forms ofholders for carrying sample receptacles and various reagent containersthat can be accessed by a substance transfer device. Examples of a loadstation and receptacle holder that can be used with embodiments areillustrated and described by Clark et al. in U.S. Pat. No. 8,309,036. Inan embodiment where the first module 100 comprises a platform forperforming a NAT, reaction reagents may comprise target capturereagents, lysis reagents, nucleic acid amplification reagents (e.g., thepolymerases and nucleoside triphosphates needed for amplification),and/or nucleic acid detection reagents, such as detectable probes orintercalating dyes.

In some embodiments, the first module 100 may further comprisetemperature ramping stations 110 configured to hold one or more reactionreceptacles in an environment that is maintained at higher than ambienttemperatures so as to raise the temperature of the contents of thereceptacles. Exemplary temperature ramping stations are disclosed byAmmann et al. in U.S. Pat. No. 8,192,992.

In some embodiments, the first module 100 may further include one ormore heater modules. The illustrated first module 100 includes threeheated incubators 112, 114, 116, each of which is configured to receivea plurality of reaction receptacles and maintain the receptacles in anelevated temperature environment. Exemplary incubators are disclosed byMacioszek et al. in U.S. Pat. No. 7,964,413 and Heinz et al. in U.S.Patent Application Publication No. 2012/0221252. A heater module mayalternatively be a heating plate. In certain embodiments, it is possibleto have a heater module configured with one or more heated incubatorsand one or more heating plates.

Also, in an embodiment in which the first module 100 comprises aplatform for performing a NAT, the first module may includesample-processing components, such as magnetic separation wash stations118, 120, adapted to separate or isolate a target nucleic acidimmobilized on a magnetically-responsive solid support from theremaining contents of the receptacle. Exemplary magnetic separation washstations are disclosed by Hagen et al. in U.S. Patent ApplicationPublication No. 2010/0288395 and Ammann et al. in U.S. Pat. No.6,605,213.

Although not exemplified in the plan drawings of first module 100, thefirst module 100 may comprise one or more substance transfer devices,for example, robotic pipettors, in some embodiments. FIG. 21, which is aperspective view of the robotic pipettor of the second module 400,exemplifies at least one way to configure a substance transfer devicefor the first module 100.

In some embodiments, the first module 100 may further include chillermodules 122 adapted to receive one or more reaction receptacles and holdthe receptacles in a lower than ambient temperature environment so as toreduce the temperature of the contents of the receptacles.

And in some embodiments, the first module 100 may include a detector 124configured to receive a reaction receptacle and detect a signal (e.g.,an optical signal) emitted by the contents of the reaction receptacle.In one implementation, detector 124 may comprise a luminometer fordetecting luminescent signals emitted by the contents of a receptacleand/or a fluorometer for detecting fluorescent emissions. The firstmodule 100 may also include one or more signal detecting devices, suchas fluorometers, coupled to one or more of the incubators 112, 114, 116and which are configured and controlled to detect, preferably atspecified, periodic intervals, signals emitted by the contents of thereceptacles contained in the incubator while a process, such as nucleicacid amplification, is occurring within the reaction receptacles. Anexemplary luminometer and an exemplary fluorometer are disclosed byMacioszek et al. in U.S. Pat. No. 7,964,413 and another exemplaryfluorometer is disclosed by Heinz et al. in U.S. Patent ApplicationPublication No. 2012/0221252.

The first module 100 further includes a receptacle transfer device,which, in the illustrated embodiment, comprises a receptacle distributor150. The components of first module 100, for example, incubators 112,114, 116, load stations 104, 106, 108, temperature ramping stations 110,wash stations 118, 120, and chiller modules 122, can also include areceptacle transfer portal through which receptacles can be insertedinto or removed from the respective components. Each component may ormay not include an openable door covering its receptacle portal. Thereceptacle distributor 150 is configured to move receptacles between thevarious components and retrieve receptacles from the components anddeposit receptacles into the components. In one exemplary embodiment,the receptacle distributor 150 includes a receptacle distribution head152 configured to move in an X direction along a transport trackassembly 154, rotate in a theta (Θ) direction, and move receptacles inan R direction into and out of the receptacle distribution head 152 andone of the components of first module 100. An exemplary receptacledistributor is disclosed by Hagen et al. in U.S. Patent ApplicationPublication No. 2012/0128451.

Second Module

Aspects of the disclosure are embodied in a second module 400 adiagnostic system. In some embodiments, the second module 400 isintegral with the first module 100, and in other embodiments, the secondmodule 400 may be selectively and operatively coupled to the firstmodule 100 as described above. In some embodiments, the first module 100to which the second module 400 can be operatively coupled include, forexample, molecular instruments, such as the Panther® instrument systemavailable from Hologic, Inc.

In one exemplary embodiment, the second module 400 is configured toperform nucleic acid amplification reactions, for example, PCR, and, incertain embodiments, to measure fluorescence in real-time (i.e., as theamplification reaction is occurring). A controller directs thecomponents of the first module 100 and components of the second module400 to perform the assay steps. In one exemplary embodiment, the firstmodule 100 houses a computer and all fluids, reagents, consumables, andmechanical modules needed to perform the specified amplification-basedassays, such as assays based on transcription-based amplificationmethods, for example, TMA or nucleic acid sequence-based amplification(NASBA). (TMA methods are described by Kacian et al. in U.S. Pat. Nos.5,399,491 and 5,480,784; and NASBA methods are described by Davey et al.in U.S. Pat. No. 5,409,818 and Malek et al. in U.S. Pat. No. 5,130,238.)As explained above, the controller may comprise a computer andpreferably can accommodate LIS (“laboratory information system”)connectivity and as well as remote user access. In some embodiments,second module 400 houses component modules that enable secondamplification assays, melting analyses, and optionally additionalfunctionalities. Other components may include a printer and an optionaluninterruptible power supply.

Embodiments of the general configuration of the second module 400 areshown in FIGS. 1, 5, 6, and 14. FIG. 1 is a perspective view ofdiagnostic system 10 comprising a second module 400 and the first module100. FIG. 5 is a top plan view of the second module 400 separated fromthe first module 100. FIG. 6 is a top plan view of an amplificationprocessing deck 430, for example, a deck containing components forperforming PCR, of the second module 400. FIG. 14 is a top plan view ofa receptacle processing deck 600 of the second module 400. Referring toFIGS. 1, 5, 6, and 14, the component of the second module 400 caninclude, for example, a substance transfer device (for example, arobotic pipettor 402), a thermal cycler/signal detector 432, tipcompartments 580 (e.g., two or more) configured to contain trays ofdisposable tips for the pipettor(s), processing cap/vial compartments440 (e.g., two or more) configured to contain trays of disposableprocessing vials and associated caps, a bulk reagent containercompartment 500, a bulk reagent container transport 550, a receptacledistribution system comprising a receptacle handoff device 602 and areceptacle distributor 312, which, in the exemplary embodiment shown,comprises a rotary distributor, MRD storage units 608, 610, 612configured to store MRDs 160, magnetic elution slots 620 (e.g., two ormore), a waste bin access door 652, a waste bin 652, a centrifuge 588, areagent pack changer 700, reagent pack loading stations (e.g., two ormore) 640, and a compartment 590 configured to store accessories,including, for example, consumables, output cards, and/orpost-processing cap/vial assemblies.

As shown in FIG. 1, the components may be positioned on differentlevels, or decks, arranged vertically through the module 400. In someembodiments, the substance transfer and handling device 402 can be arobotic pipettor 402 as shown in FIG. 1. The robotic pipettor 402 isdisposed near the top of the second module 400, above all othercomponents, in some embodiments. The depicted configurations representonly a single embodiment. The vertical order of the decks and componentsmay vary according to the intended use of diagnostic system 10. In thedepicted embodiment, below the robotic pipettor 402, the amplificationprocessing deck 430 includes the bulk reagent container compartment 500and bulk reagent container transport 520, the centrifuge 588, the top ofthe thermal cycler/signal detector 432, the tip compartments 580, andthe processing cap/vial compartments 440. Below the amplificationprocessing deck 430, the receptacle processing deck 600 includes thereceptacle handoff device 602, the rotary distributor 312, the MRDstorage units 608, 610, 612, the magnetic elution slots 620, the reagentpack changer 700, and the reagent pack loading stations 640. As can beseen in FIG. 6, the magnetic elution slots 620 and the reagent packloading stations 640 on the receptacle processing deck 600 areaccessible by the robotic pipettor 402 through a gap between modules ofthe amplification processing deck 430.

The receptacle distribution system comprising the receptacle handoffdevice 602 and the rotary distributor 312, is configured to receive areceptacle or group of receptacles (e.g., MRD 160) from the receptacletransfer device (e.g., the receptacle distributor 150) of the firstmodule 100 and transfer the receptacle to the second module 400 andconfigured to move the receptacle into different positions in the secondmodule 400. The rotary distributor 312 and the receptacle handoff device602 are shown schematically in FIG. 14. Further details regarding thesecomponents are described below.

In some embodiments, the second module 400 is operatively positionedadjacent to the first module 100, with the bulk reagent containertransport 550 extending into the first module 100 so that elutioncontainers 502, 504 can be transported by the bulk reagent containertransport 550 from the bulk reagent container compartment 500 to aposition in the first module 100 at which a substance transfer device,for example, a robotic pipettor, in the first module 100 can access thecontainers 502, 504.

In some embodiments, the second module 400 is generally self-supportingrelative to first module 100 such that the second-module/first-moduleassembly is not over-constrained. Thus, in some embodiments, the secondmodule 400 does not include any feet that contact the ground beneath thesecond module and support some or all of the weight of the module. Insome embodiments, if the second module 400 includes its own rigid feet(e.g., two, three, or four feet), the feet of the first module 100 andthe feet of the second module 400 could create an over-constrainedgeometry. In this case, one would carefully level all feet of the secondmodule 400 and the first module 100 relative to each other to ensurethat the assembly is level and that excessive stresses are not appliedto attachment points between the second module 400 and the first module100. To avoid such a potentially over-constrained geometry, the secondmodule 400, in some embodiments, is cantilevered off the first module100 if the first module feet can support the additional weight of thesecond module. In some embodiments, some of the weight of the secondmodule 400 may be supported by a single foot on a far edge of the secondmodule 400 away from the first module 100.

In some embodiments, second module 400 and first module 100 are mountedto an integral frame.

In some embodiments, the interface between the second module 400 and thefirst module 100 is blocked and sealed where possible to prevent airflowbetween the two modules. Existing air inlets on the side of the firstmodule 100 facing the second module 400 may be ducted through the secondmodule 400 to a fresh air source. The side wall of the second module 400facing the first module 100 can be covered by panels to block airflowinto the first module 100. Such panels can include openings wherenecessary for receptacle or container transfer between the second module400 and first module 100, cable routing, etc.

Components of exemplary embodiments of the second module 400 aredescribed below.

Reagent Packs

In some embodiments, amplification reagents and other reagents may beprovided in the second module 400 in lyophilized form in a reagent packcomprising a cartridge that includes wells within which the lyophilizedreagent may be reconstituted. Examples of cartridges that can be used inthis embodiment are disclosed by Knight et al. in U.S. ProvisionalApplication No. 61/782,320, “Systems, Methods, and Apparatus forPerforming Automated Reagent-Based Assays,” filed Mar. 14, 2014, whichenjoys common ownership herewith (these cartridges are both identifiedby reference number 500 in FIGS. 10A and 10B). The reagent pack isfurther configured to be stored within the second module 400 and, insome embodiments, to be moved within the second module 400 by thedistributor 312, and inserted and removed from the reagent pack changer700.

Details of a reagent pack 760, according to one embodiment, are shown inFIGS. 19 and 20. The reagent pack 760 may include a plurality of mixingwells 762, each of which contains a lyophilized unit-dose,assay-specific reagent 768, which may be in pellet form. (As usedherein, “unit-dose” or “unitized” means an amount or concentration of areagent sufficient to perform one or more steps of a single assay for asingle sample.) In some embodiments, the unit-dose reagent 768 comprisesa component for performing a nucleic acid amplification reaction. Forexample, the nucleic acid amplification reaction component can be apolymerase, nucleoside triphosphates, or any other suitable component.In the illustrated embodiment, the reagent pack 760 includes ten mixingwells 762. But in some embodiments, the reagent pack 760 may includemore or fewer than ten mixing wells. Each mixing well 762 of a singlereagent pack 760 may hold the same reagent, or the wells 762 may holddifferent reagents, or some wells 762 may hold the same reagent and somemay hold different reagents. Exemplary assay specific reagents 768 heldin the reagent pack 760 include unitized reagents for performing asingle amplification reaction, for example, PCR and/or a detectionreaction utilizing a sample. Such reagents may be specific for onetarget nucleic acid or a plurality of different target nucleic acids.For example, the plurality of different target nucleic acids may be partof a respiratory panel, and the unitized reagents are sufficient toconduct a PCR reaction targeting Flu A, Flu B, RSV, parainfluenza 1, 2,and 3, Human Metapneumovirus, Adenoviris, H1, H3, 2009 H1N1, and/orTamiflu resistance. In an embodiment, each reagent pellet 768 is held atthe bottom of the associated mixing well 762 with an electrostaticcharge imparted to the pellet 768 and/or the mixing well 762. In otherembodiments, each reagent pellet 768 is held at the bottom of theassociated mixing well 762 with one or more physical feature present inthe mixing well 762, for example, those disclosed by Knight et al. inU.S. Provisional Application No. 61/782,320.

In some embodiments, the mixing wells 762 are covered by a pierceablefoil 766 adhered to the top of the reagent pack 760. Foil 766 can bepierced by a pipette tip 584 to enable reconstitution agents or othersubstances to be dispensed into the mixing well 762 and to enablereconstituted reagent to be aspirated from the mixing well 762.

In some embodiments, the reagent pack 760 further includes amanipulating structure 764, for example, a manipulating hook, that issimilar to the manipulating structure 166 of the MRD 160 and isconfigured to be engageable by a manipulating structure, for example, ahook, of the rotary distributor 312. The reagent pack 760 may include arear recess 770 that is configured to align the reagent pack within areagent pack carrier, as will be described below.

Tip Compartments

As shown in FIGS. 1, 5, and 6, tip compartments 580 are configured tohold trays 582 of disposable pipette tips in a manner that enables thetips held in the drawers 580 to be accessed by the robotic pipettor 402.In the illustrated embodiment, the second module 400 includes two tipcompartments 580, each configured to hold up to three trays 582 ofdisposable pipette tips. The compartments 580 may be configured toaccept commercially-available trays of disposable pipette tips.Exemplary, commercially available pipette tips and trays are availablefrom TECAN (TECAN U.S. Inc., Research Triangle Park, N.C.). Such tipsare available in a variety of volumetric capacities, and each tip may beconductive to facilitate capacitive liquid level sensing and tip-presentdetection, as is well known in the art. Exemplary trays hold ninety-sixpipette tips.

The tip compartments 580 are configured to be accessible to an operatorfor reloading of trays 582. In one contemplated embodiment, the tipcompartment 580 comprises a drawer configured to be pulled out of thesecond module 400 to enable an operator to place the trays 582 of tipsinto the drawers 580 and to remove empty trays from the drawers 580. Adoor or cover panel that is either part of each drawer 580 or thehousing of diagnostic system 10 is opened to access each tip compartment580 behind it. The door or cover panels may provide an estheticallypleasing appearance to the front of the second module 400. Manual orautomated locks, controlled by the system controller, may be provided toprevent the compartment 580 from being opened when the second module 400is operating. In some embodiments, visible and/or audible warningsignals may be provided to indicate that a compartment 580 is not closedproperly. In an alternative embodiment, compartment 580 comprises anaccess door and a slidable tray, wherein the tray is configured to slideout from second module to thereby provide loading access to an operator.

Substance Transfer and Handling System

The substance transfer and handling system 402, for example, a roboticpipettor, shown in FIGS. 1, 21, and 22 is a dual arm system comprising afront arm 408 and a back arm 416. However, other robotic pipettor andhandling configurations are contemplated, and the presently depictedembodiment is only exemplary. Substance transfer and handling system 402can be configured to dispense and/or aspirate substances into and/orfrom a container, receptacle, well, etc., in second module 400. In anexemplary embodiment, the front arm 408 includes a substance transferpipettor 410 configured to aspirate fluid and dispense fluid andincludes a pump, for example, an integrated syringe pump, and the backarm 416 includes a vial transfer arm 418 and does not perform substancetransfer. The robotic pipettor system 402 comprises a Cartesian gantryassembly with two transverse tracks 404, 406, a back arm longitudinaltrack 420, and a front arm longitudinal track 412. The designations“longitudinal” and “transverse” are merely for distinguishing the twosets of tracks, which may be orthogonal to one another, but otherwisethe designations are arbitrary.

The substance transfer pipettor 410 may be driven back and forth alongthe front arm longitudinal track 412 by a belt, drive screw, or othermotion transmission device coupled to a motor, and the vial transfer arm418 may be driven back and forth along the back arm longitudinal track420 by a belt, drive screw, or other motion transmission device coupledto a motor. The front arm longitudinal track 412 may be driven back andforth along the transverse tracks 404, 406 by a belt, drive screw, orother motion transmission device coupled to a motor, and the back armlongitudinal track 420 may be driven back and forth along the transversetracks 404, 406 by a belt, drive screw, or other motion transmissiondevice coupled to a motor. The substance transfer pipettor 410 and thevial transfer arm 418 include probes that are driven along the Z, orvertical, axis, for example, by a motor coupled to the probes, e.g., bya gear, a rack and pinion, a lead screw, or other suitable device. Themotors may be under the control of a system controller. The motors maybe stepper motors and may include rotary encoders for controlling andmonitoring the position of the track or pipettor to which it is coupled.Each of the tracks has home sensors (or limit switches) for indicatingwhen the substance transfer pipettor 410 or the vial transfer arm 418 isin one or more designated positions, such as a designated “home”position. Similarly, each device may have a vertical home sensor forindicating when the probe is in one or more designated verticalpositions, such as a designated vertical “home” position. Such sensorsfor indicating a home position may include optical sensors (e.g.,slotted optical sensors), proximity sensors, magnetic sensors,capacitive sensors, etc.

In one exemplary embodiment, the substance transfer pipettor 410 isconfigured to accept TECAN 1 mL disposable pipette tips by inserting theprobe thereof into a disposable pipette tip, and an interference fitbetween the probe and the pipette tip frictionally secures the pipettetip to the end of the probe. The front arm 408 and the substancetransfer pipettor 410 are configured to access at least parts of boththe amplification processing deck 430 and the receptacle processing deck600 on the second module 400. The substance transfer pipettor 410 mayinclude integrated tip sensing for confirming the presence or absence ofa disposable pipette tip, capacitive level sensing for detecting contactby the pipette tip with the surface of the fluid contents of a reactionreceptacle or other container and determining the level of the fluidcontents based on the detected vertical position of the pipettor, andpressure sensing for sensing pressure fluctuations within the substancetransfer system during fluid dispensing or aspiration. The substancetransfer pipettor 410 is capable of transferring fluids, caps, orcap/processing vial assemblies such as those described below.

The vial transfer arm 418 is a “pick and place” device configured pickup a cap/vial assembly by inserting the probe thereof into a cap that iscoupled to a vial, as will be described below.

Pipettor Pump

In an exemplary embodiment, the pump for the substance transfer pipettor410 comprises a ceramic piston driven by a servomotor and a lead screw.The servomotor is controlled by the system controller, and the devicecan include rotary encoder feedback to the system controller and homesensors for monitoring the position of the piston. The syringe may havea volume of between 0.5 and 3 mL (preferably 1.05 mL) and, in certainembodiments, is a ceramic. The pump can preferably dispense very smallvolumes (5 μL) of fluid with +/−5% coefficient of variation (CV)measured across 30 discrete dispenses. To achieve this performance, incertain embodiments, the pump includes a solenoid valve to releasepressure at the end of the stroke to ensure consistent fluid shear.

Processing Cap/Vial Assembly

In general, the processing vial provides a receptacle for containingreaction fluids for performing PCR or other process. The cap isconfigured to be placed into or onto the vial in an automated manner soas to close off the vial. In some embodiments, the cap is configured toreceive the end of the vial transfer arm 418 with a friction fit, sothat the transfer arm 418 can thereafter pick up the cap and place itinto or onto the vial. The cap and vial are configured to lock togetherso that, once the cap is placed into or onto the vial, the cap and thevial are interlocked to form a cap/vial assembly. The robotic pipettor,with the probe of the transfer arm 418 inserted into the cap, can thenpick up the cap/vial assembly and transfer it from one location withinthe second module 400 to another location. Exemplary caps and processingvials are disclosed by, for example, Knight et al. in U.S. ProvisionalApplication No. 61/782,320.

Details of an exemplary embodiment of the processing vial 464, theprocessing vial cap 476, and a vial transfer arm probe 422 (which may bethe probe of the substance transfer pipettor 410 or the vial transferarm 418) are shown in FIGS. 23-25.

In the embodiment shown in FIGS. 23-25, the processing vial 464 may havea conical shape and an open top end 465 surrounded by a locking collar466. Lateral through holes 468 are formed through the locking collar 466at diametrically opposed locations. A latch hook 472 is located aboveeach through hole 468.

The processing vial cap 476 has an open top end 478 and a closed lowerend 480. An annular collar 482 extends about the cap 476 at a positionbetween the top end 478 and lower end 480. Collar 482 of the vial 476sits atop the thermal cycler when the vial 476 is placed therein,ensuring a close fit of the vial within the wells of the thermal cycler.An exemplary thermal cycler for use with processing vial 476 isdisclosed by Buse et al. in U.S. Patent Application Publication No.2014/0038192. A lower portion of the cap 476 beneath the collar 482defines a plug that fits into the open top end 465 of the processingvial 464. This plug is sized so as to fit into the processing vial 464with an interference, friction fit. A latch collar 484 extends about thecap 476 at a position below the collar 482. Seal rings 486, 488 extendabout the cap 476 at positions below the latch collar 484.

FIGS. 24 and 25 show, in cross-section, a processing vial cap 464,initially held in a cap well 490 of a cap/vial tray 460, and aprocessing vial 464 held in a vial well 474 of the cap/vial tray 460.After fluids are dispensed into the processing vial 464 with thedisposable pipette tip 584 (connected to a robotic pipettor), theprocessing vial 464 is capped by a processing vial cap 476 by insertingthe closed lower end 480 of the cap 476 into the open top end 465 of thevial 464, until a bottom surface of the collar 482 of the cap 476 abutsa top surface of the locking collar 466 of the vial 464. The latchcollar 484 of the cap 476 snaps in beneath the latch hooks 472 of thevial 464 to secure the cap 476 to the vial 464. The cap 476 and the vial464 are thereafter locked together and the cap/vial assembly may bepicked up and moved by the pipettor. The cap/vial assembly can beremoved from the pipettor probe 422 by an eject device engaging a rim479 surrounding open end 478 to pull the cap/vial assembly off the probe422. The seal rings 486, 488 of the cap 476 preferably have outerdiameters that are slightly larger than the inner diameter of the upperportion of the vial 464, thereby forming a tight seal between the cap476 and the vial 464 as the cap and vial are made of materials, such assuitable plastics, that are at least partially resilient.

An alternative processing cap/vial assembly is shown in FIG. 26 , whichis an exploded perspective view of a processing vial 1100 and aprocessing vial cap 1200. Processing vial cap 1200 includes closed lowerend 662, a tapered opening 1215, and a latch collar 1240 having latchfingers 1250. The vial 1100 includes a lock collar 1155 surrounding theopen top end of the vial 1100 and a collar 1125. Collar 1125 of vial1100 sits atop the thermal cycler when the vial 1100 is placed therein,ensuring a close fit of the vial within the wells of the thermal cycler.After fluid is dispensed into the vial 1100, the vial is capped by firstinserting the pipettor probe 422 into the tapered opening 1215 of theprocessing vial cap 1200 to frictionally secure the cap 1200 to thepipettor probe 422 and then picking up the cap 1200 with the pipettorand inserting the closed lower end 662 of the cap 1200 into the open topend of the vial 1100 until the latch fingers 1250 lockingly snap ontothe lock collar 1155 of the vial 1100. The cap 1200 and the vial 1100are thereafter locked together and the cap/vial assembly may be pickedup and moved by the pipettor. The cap/vial assembly can be removed fromthe probe 422 by an eject device engaging a rim 1225 surrounding opening1215 to pull the cap/vial assembly off the probe 422.

Details of the vial and cap of FIG. 26 are shown in FIGS. 45-55.

As shown in FIGS. 45-48, the vial 1100 is a single-piece receptacle thatincludes a body 1105 having a generally cylindrical upper portion 1110and a tapered lower portion 1120. Formed on an outer surface of the body1105 is collar 1125, which separates the upper and lower portions of thebody. The upper portion 1110 of the body 1105 has an open end 1145through which fluid samples are deposited or removed from the vial 1100.The tapered lower portion 1120 has a closed end 1150 that may either beflat or rounded to provide optical communication with an optical system,for example, one or more optical fibers (not shown) of a biochemicalanalyzer. In various embodiments, the bottom surface of the closed-endedlower portion may be flat or curved.

The vial 1100 optionally containing a sample or reaction mixture isconfigured for insertion into a receptacle holder of an automatedbiochemical analyzer (not shown). As used herein, a receptacle that is“configured for insertion” refers to the exterior surface of the body1105 of the vial 1100 being sized and shaped to maximize contact betweenthe receptacle and a receptacle well of a receptacle holder. In certainembodiments, this maximal contact refers to physical contact of thereceptacle well with at least a portion of the vial 1100. Also incertain embodiments, this maximal contact refers to physical contact ofthe receptacle well with the tapered lower portion 1120 of the vial1100, or at least a portion the tapered lower portion 1120 of the vial1100.

Formed in the inner surface 1140 of the upper portion 1110 of the body1105 is one or more longitudinally oriented grooves 1135 to facilitatethe venting of air displaced from the interior upon deposit of the testsample or attachment of a cap 1200 to the vial 1100. In variousembodiments, a plurality (i.e., 2, 3, 4, 5, 6, 7, or 8) oflongitudinally oriented grooves may be formed in the inner surface 1140of the upper portion 1110, and the grooves 1135 may be equally spacedapart from one another around the entire circumference of the body 1105.

Circumscribing the open end 1145 of the upper portion 1110 of the body1105 is lock collar 1155 extending radially outward from a central axisthereof. In various embodiments, the lock collar 1155 tapers from theouter-most portion of the radially-extended lip towards the open end ofthe body, and is configured for securable attachment to a cap 1200(FIGS. 49-55).

With reference now to FIGS. 49-52, the securable cap 1200 includes lowerportion 1220 having an outer surface for sealing engagement of the innersurface 1140 of the upper portion 1110 of the vial 1100 and an upperportion 1210. To ensure an essentially leak-proof seal when the cap 1200is securely attached to the open end 1145 of the upper portion 1110 ofthe vial 1100, the outer surface of the lower portion 1220 of the cap1200 is formed with one or more annular flanges 1230 for contacting theinner surface 1140 of the upper portion 1110 thereof. In variousembodiments, the lower portion 1220 of the cap 1200 is formed with 1, 2,or 3 annular flanges 1230 for contacting the inner surface 1140 of theupper portion 1110 of the vial 1100.

The upper portion 1210 of the cap 1200 includes tapered opening 1215 forfrictional attachment to a receptacle transport mechanism 422 (FIG. 26),such as a pipettor or pick-and-place robot. Guiding insertion of thereceptacle transport mechanism 422 into the open end 1215 of the upperportion 1210 of the cap 200 are one or more linear ribs 1260 formed inthe inner surface 1270 of the upper portion 1210. The linear ribs 1260protrude towards an axial center of the cap 1200, thereby decreasing theinner fitment diameter of the upper portion 1210 of the cap 1200. Theselinear ribs 1260 can, among other things, enhance the frictionalattachment to the receptacle transport mechanism 422. In variousembodiments, 1, 2, 3, 4, 5, 6, 7, or 8 linear ribs 1260 are formed inthe inner surface 1270 of the cap 1200 and extend at least a portion ofthe way down the length of the upper portion 1210 thereof.

At least one of the linear ribs 1260 may be formed with a portion 1265thereof that gradually tapers radially inward toward a central axis ofthe upper portion 1210 of the cap. In other words, the amount ofprotrusion of the linear rib 1260 may gradually increase in size as thelinear rib 1260 approaches the bottom 1245 of the upper portion 1210 ofthe cap 1200. Alternatively, or in addition thereto, in certainembodiments, the linear rib 1260 may gradually increase in overallthickness as it approaches the bottom 1245 of the upper portion 1210 ofthe cap 1200. Thus, gradual increase in thickness or radial geometry iscontemplated for the gradual tapering of the one or more linear ribs1260, which serves to stabilize and center the receptacle transportmechanism 422 as it is lowered into the cap 1200 for transport.

Corresponding with each linear rib 1260 and disposed on the exteriorsurface of the upper portion 1210 of the cap 1200 are one or moreindentations 1230 that extend along at least part of the length thereof.The indentations may be formed in any shape such as, for example,concave, notched, squared, etc. Thus, at least one indentation 1230 isformed in the exterior surface of the upper portion 1210 of the cap12001200. In various embodiments, the length of the indentation 1230 isthe same as the length of the corresponding linear rib 1260, and eachlinear rib 1260 is positioned such that it lies on the inner surface1270 of the cap 1200 in a location that directly opposes the position ofthe at least one indentation 1230 formed on the outer surface of the cap12001200 in a one-to-one relationship. The coupling of a linear rib 1260with an indentation in this manner enhances the predictability of thefrictional attachment of the cap 1200 to a receptacle transportmechanism 422. In certain embodiments, as the receptacle transportmechanism 422 is lowered into the open end 1215 of the cap 1200, itcontacts the one or more linear ribs 1260, thereby pressing against theone or more linear ribs 1260. Such pressing against the linear ribs 1260causes the cap 1200, and indentations 1230 to flex and/or expandradially outward with respect to the axial center thereof to accommodatethe receptacle transport mechanism 422 and enhance fictional attachmentthereto. Accordingly, 1, 2, 3, 4, 5, 6, 7, or 8 indentations 1230 may beformed on the exterior surface of the upper portion 1210 of the cap1200.

Circumscribing the opening 1215 of the upper portion 1210 of the cap1200 is the rim 1225 extending radially outward from a central axisthereof. In various embodiments, the rim 1225 tapers from the open end1215 towards the lower portion 1220. Protruding from the taper of therim 1225 are a plurality of protrusions 1235. The protrusions 1235 maybe equally spaced apart from one another and facilitate stacking and/ordocking within a well of a consumable card for use in an automatedbiochemical analyzer. In various embodiments, 1, 2, 3, 4, 5, 6, 7, or 8protrusions 400 are formed in the taper of the rim 1225.

Separating the upper portion 1210 from the lower portion 1220 of the cap1200 is the latch collar 1240 that extends radially away from an axialcenter thereof. The latch collar 1240 includes the plurality of lockingfingers 1250 that extend from the latch collar 1240 toward the lowerportion 1220 of the cap 1200. The locking fingers 1250 are shaped forsecurely engaging the lock collar 1155 of the vial 1100, and may bedisposed to allow for removable attachment of the cap 1200 to the vial1100, while maintaining a leak-proof seal of the contents thereof. Invarious embodiments, 1, 2, 3, 4, 5, 6, 7, or 8 locking fingers 1250 areformed in the cap 1200.

The latch collar 1240 of the cap 1200 additionally serves to form abottom 1245 to separate the upper portion 1210 from the lower portion1220, thereby closing the interior of the vial 1100 from theenvironment. However, in certain embodiments, the bottom 1245 is scored1255 for piercing by a mechanism for collecting and/or adding reagentsto the test sample within the vial 1100. Such piercing avoids the needto remove the secured cap 200 from engagement with the vial 1100, whileproviding access to the contents therein.

The vial 1100 and cap 1200 of the present invention may be prepared froma number of different polymer and heteropolymer resins, including, butnot limited to, polyolefins (e.g., high density polyethylene (“HDPE”),low density polyethylene (“LDPE”), a mixture of HDPE and LDPE, orpolypropylene), polystyrene, high impact polystyrene and polycarbonate.An example of an HDPE is sold under the tradename Alathon M5370 and isavailable from Polymerland of Huntsville, N.C.; an example of an LDPE issold under the tradename 722 and is available from The Dow ChemicalCompany of Midland, Mich.; and an example of a polypropylene is soldunder the tradename Rexene 13T10ACS279 and is available from theHuntsman Corporation of Salt Lake City, Utah. Although LDPE is a softer,more malleable material than HDPE, the softness of LDPE providesflexibility in the locking arms 1250 of the cap 1200 to securably engagethe lip 1155 of the vial 100. And, while a cap made of HDPE is morerigid than one made of LDPE, this rigidity tends to make an HDPE capmore difficult to penetrate than one made of LDPE. It should beunderstood that the vial 1100 and cap 1200 may be comprised of acombination of resins, including, for example, a mixture of LDPE andHDPE, preferably in a mixture range of about 20% LDPE: 80% HDPE to about50% LDPE: 50% HDPE by volume. In addition, the amounts of LDPE and HDPEused to form each of the vial 1100 and cap 1200 may be the same ordifferent. In various embodiments, at least a portion of the cap 1200 isformed from an opaque material having low to no autofluorescensecharacteristics. Also, in certain embodiments, the portion of the cap1200 formed from an opaque material having low to no autofluorescensecharacteristics is at least the lower portion 1220 thereof, includingthe inner surface 1232 of the lower portion 1220 of the cap 1200.

Regardless of the type or mixture of resins chosen, the vial 1100 andcap 1200 are preferably injection molded as unitary pieces usingprocedures well-known to those skilled in the art of injection molding,including a multi-gate process for facilitating uniform resin flow intothe receptacle and cap cavities used to form the shapes thereof. Uniformresin flow is desirable for achieving consistency in thickness, which isimportant for a variety of reasons, including for the penetrable bottom1245 of the cap 1200; to ensure a secure, such as an air-tight,engagement of the cap 1200 and vial 1100; to ensure a predictableengagement of the cap 1200 with the receptacle transport mechanism 422;and to ensure maximal contact of the vial 1100 with a receptacle well ofa receptacle holder.

The second module 400 may include “vial present” sensors. The vialpresent senor is used as a process control measure to verify that a vialis attached to the cap. The substance transfer pipettor 410 (front arm408) and the vial transfer arm 418 (back arm 416) will detect when a capis attached to the arm. One way substance transfer pipettor 410 or thevial transfer arm 418 will detect when a cap is present is by a stripsleeve on the probe 422. When the cap is picked by the probe, the upperrim of the cap pushes on and raises the sleeve (e.g., a fewmillimeters), and this movement may be detected by a sensor. However,pipettors often cannot detect if a vial is attached to the cap. In oneexemplary embodiment, the vial present sensor is an optical sensor (ormultiple sensors) that either arm 408, 416 can move past/through as ittransports a capped vial into or out of the centrifuge 588. The vialpresent sensor will trigger on the vial (if present) as the arm movespast the sensor.

Bulk Reagent Container Compartment and Bulk Reagent Container Transport

In one exemplary embodiment, the bulk reagent container compartment 500is configured to hold a plurality of bulk reagent containers. Each bulkreagent container can hold a reagent for use in multiple reactionreceptacles. In some embodiments, the bulk reagent containers arebottles or any other container suitable for containing reagents in bulk.In some embodiments, the bulk reagents within the bulk reagentcontainers can include a sample preparation reagent (e.g., targetcapture reagent (TCR), a wash solution, an elution reagent, or any othersample preparation reagent), a reconstitution reagent, or any otherrequired bulk reagent. In some embodiments, the bulk reagent containershold a quantity of the bulk reagent sufficient to perform between about50 to 2000 assays. In some embodiments, the bulk reagent containers holda quantity of the bulk reagent sufficient to perform between about 250to 1000 assays. In some embodiments, the bulk reagent containers hold aquantity of the bulk reagent sufficient to perform less than about 250assays, or more than about 1000 assays. In some embodiments, the bulkreagents are for performing isothermal nucleic acid amplificationreactions, for example, a transcription-based amplification reactionsuch as TMA.

In some embodiments, the bulk reagent container compartment 500 can beconfigured to hold two elution buffer containers, two oil containers,and four reconstitution fluid containers. The bulk reagent containercompartment 500 may be opened by an operator to load containers. Forexample, bulk reagent container compartment 500 may be a drawer that isslid out from the main body of diagnostic system 10. In someembodiments, once closed, the bulk reagent container transport 550 movesthe elution buffer containers into the first module 100 to a location inwhich a substance transfer mechanism, for example, a robotic pipettor,can access the containers. In some embodiments, the bulk oil containersand the bulk reconstitution fluid containers remain in the bulk reagentcontainer compartment 500, where they are accessible to the substancetransfer pipettor 410.

Containers carried on the bulk reagent container compartment 500 may beidentified by machine-readable code, such as RFID. An indicator panel507 having visible (e.g., red and green LEDs) and/or audible indicatorsprovides feedback to the operator regarding container status.

The bulk reagent container compartment 500 and bulk reagent containertransport 550 are shown in FIGS. 5-10. In some embodiments, the bulkreagent container compartment 500 is located on the amplificationprocessing deck 430 adjacent the tip compartments 580 and may beaccessed from the front of the second module 400. The bulk reagentcontainer compartment 500 may be pulled out to enable an operator toplace two containers 502, 504 containing an elution buffer as well as anumber of bulk containers, or other types of fluid containers,containing other reagents, such as, for example, oil or reconstitutionbuffer, into the drawer 500. The number of containers accommodated bythe drawer 500 is dictated by considerations of intended throughput anddesired time period between required re-stocking of supplies.

A door or cover panel, which is either part of the bulk reagentcontainer compartment 500 or the housing of diagnostic system 10 isopened to access the bulk reagent container compartment 500 behind it.The door or cover panel can provide an esthetically pleasing appearanceto the front of the second module 400. Automated locks, controlled bythe system controller, may be provided to prevent the bulk reagentcontainer compartment 500 from being pulled open when the second module400 is operating. In some embodiments, visible and/or audible warningsignals may be provided to indicate that the bulk reagent containercompartment 500 is not closed properly.

When the bulk reagent container compartment 500 is closed, thecontainers 502, 504 are moved to the far end of the drawer 500, wherethey are positioned in operative engagement with the bulk reagentcontainer transport 550 extending laterally from an end of the drawer500 into the first module 100. Upon closing the bulk reagent containercompartment 500, the bulk reagent container transport 550 is activatedto move the containers 502, 504 into the first module 100 to a positionat which the robotic pipettor of the first module 100 can access thecontainers 502, 504. The bulk reagent container transport 550 may beactivated manually by an operator (e.g., pressing a button or switch) orautomatically by the system controller upon receipt of an input signalindicating that the bulk reagent container compartment 500 has beenfully closed, thereby placing the containers 502, 504 into operativeposition with respect to the bulk reagent container transport 550.

Details of the bulk reagent container compartment 500 are shown in FIGS.9-13. In some embodiments, the bulk reagent container compartment 500includes a container tray 506 configured to hold the plurality ofreagent containers, and a container carriage 512 disposed at the end ofthe container tray 506 and configured to carry elution reagentcontainers 502, 504. In some embodiments, the container tray 506 and thecontainer carriage 512 are moveable along a track 508 between awithdrawn position as shown in FIG. 9 (see also FIG. 7) and a closedposition as shown in FIG. 10 (see also FIG. 8).

The container carriage 512 is carried on a carriage transport 522configured to be movable with the container tray 506 along the track508. As shown in FIGS. 11 and 12, the carriage transport 522 includeshorizontal carriage rails 524 and 526 that engage rail slots 514, 516,respectively, formed in the container carriage 512 to retain thecontainer carriage 512 within the carriage transport 522.

The bulk reagent container compartment 500 is configured to permit anoperator to place reagent containers 502, 504 within the containercarriage 512 when the drawer is in the open position, as shown in FIGS.7 and 9. Upon closing the drawer, to the position shown in FIGS. 8 and10, the reagent container carriage 512 can be released from the carriagetransport 522 and engaged by the bulk reagent container transport 550 topull the carriage 512 to a lateral position with respect to the track508 of the container tray 506, as shown in FIG. 10. In this manner, itis possible to transfer bulk reagents from the second module 400 to thefirst module 100.

More particularly, the carriage transport 522 moves along the track 508as the container tray 506 is moved into the open or closed positions. Asshown in FIG. 11, the carriage transport 522 includes a pivotingcarriage lock 532 configured to pivot about pivot pin 534 and includinga locking leg 536 that extends upwardly through an opening 528 formed inthe bottom of the carriage transport 522 and into a lock recess 520formed in the bottom of the container carriage 512. A trigger leg 538extends below the carriage transport 522. As the container tray 506 ismoved into the closed position (to the left in FIG. 11) the trigger leg538 of the pivoting carriage lock 532 engages a lock trigger 510projecting upwardly from the track 508, thereby causing the carriagelock 532 to pivot counterclockwise, as shown in FIG. 12, to withdraw theend of the locking leg 536 from the lock recess 520 of the containercarriage 512. With the trigger leg 538 withdrawn from the lock recess520, the container carriage 512 and the containers 502, 504 carriedtherein, are able to slide laterally out of the carriage transport 522and onto the bulk reagent container transport 550.

The bulk reagent container transport 550 includes a powered carriagetransport mechanism for moving the container carriage 512 and containers502, 504. In one exemplary embodiment, as shown in FIGS. 9, 10, and 13,the carriage transport comprises motor 552 and a continuous belt 554disposed over the output shaft of the motor and an idler wheel 556located on an opposite end of the container transport 550 from the motor552. Motor 552 may comprise a stepper motor and may include a rotaryencoder for monitoring and controlling, via control signals and feedbackdata, the position of the motor.

The carriage transport mechanism further includes a sled 558 with acarriage hook 564 extending therefrom. The belt 554 is attached to aportion of the sled 558 so that movement of the belt by the motor 552causes a corresponding translation of the sled 558 in one direction orthe other along the transport 550.

As shown in FIGS. 12 and 13, as the container tray 506 is moved to aclosed position in which the trigger leg 538 of the pivoting carriagelock 532 engages the lock trigger 510 to withdraw the locking leg 536from the lock recess 520, the carriage hook 564 passes into a carriagehook slot 530 formed in the carriage transport 522 and engages a hookcatch 518 formed in the container carriage 512. The sled 558 andcarriage hook 564 may then be translated laterally along the containertransport 550 by the belt 554 to pull the container carriage 512 off ofthe carriage transport 522 and onto the bulk reagent container transport550. As shown in FIG. 11, the bulk reagent container transport includescarriage rails 566, 568 that will engage the rail slots 514, 516,respectively, of the container carriage 512 as the container carriage512 is pulled onto the bulk reagent container transport 550.

As shown in FIG. 13, a home flag 560 projects from the sled 558 andengages a slotted optical sensor 562 to indicate that the sled 558 andthe carriage hook 564 are in the fully-extended position shown in FIG.13. A second slotted optical sensor 570 is provided closer to the motor552 (see FIG. 9). The second optical sensor 570 is engaged by the homeflag 560 when the sled 558 and hook 564 are in the fully retractedposition, as shown in FIG. 9. Signals from the sensors 562, 570 arecommunicated to a system controller to monitor the position of the sled558. Alternatively, the bulk reagent container transport 550 may includelimit switches (e.g., contact switches) to stop operation movement ofthe sled 558 at the fully extended and/or fully retracted positions, forexample, by generating stop signals communicated to a controller whichthen sends stop commands or terminates power to the motor 552. Stillother types of sensors may be used for indicating extended and retractedstop positions, including proximity sensors, magnetic sensors,capacitive sensors, etc.

Cycler/Signal Detector

Cycler deck 430 comprises cycler/detector 432, such as, for example, athermal cycler. The cycler 432 is used in nucleic acid amplificationreactions and the selection of cycler type depends on the nature of theamplification reaction intended to be run on the second module 400. Forpurposes of the present disclosure, exemplification will be made using athermal cycler. However, it is understood that the cycler typeincorporated into the second module 400 depends on the amplificationreaction intended to be run on the second module 400.

An exemplary embodiment of a thermal cycler 432 is disclosed by Buse etal. in U.S. Patent Application Publication No. 2014/0038192. Anexemplary embodiment of a signal detector 432 is disclosed by Hagen etal. in U.S. Pat. No. 9,465,161, “Indexing Signal Detection Module,”filed Mar. 7, 2014, which enjoys common ownership herewith.

In certain embodiments, the thermal cycler can have different thermalzones. Such thermal cyclers allow the system to run separate assaysunder different conditions. For example, in a two zone thermal cycler, afirst assay can be run under a first set of time and temperatureconditions and a second assay can be run under a second set of time andtemperature conditions. It is contemplated that the multi-zone thermalcycler can have two, three, four, five, or even six or more separatethermal zones. Generally, to the extent that a multi-zone thermal cycleris implemented in the system, the number of zones for the multi-zonethermal cycler is evenly divisible into 96 (i.e., 2, 4, 6, 8, etc.)

Receptacle Holder

In an exemplary aspect, cycler 432 comprises an apparatus 2100 toperform the heating (i.e., isothermal or temperature cycling) necessaryfor a nucleic acid amplification assay. As shown in FIG. 56, theapparatus 2100 includes one or more (i.e., 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, or any whole number between 1 and 20, or more) receptacleholders 2110 (see also FIGS. 57-61). In an exemplary embodiment, theapparatus 2100 includes two or more receptacle holders 2110. Such anapparatus may include a housing 2050 (see FIG. 57) within which the oneor more receptacle holders 2110 are located. The housing 2050 may bemade from any suitable structural material such as, for example, plasticor metal.

When multiple receptacle holders 2110 are provided in an apparatusdescribed herein, each receptacle holder 2110 disposed within theapparatus may be disposed in alignment with one another to facilitatethe automated processing steps involved in nucleic acid amplificationassays. It should be understood that any alignment may be used inaccordance with the size and shape of the apparatus. In an exemplaryembodiment, the receptacle holders are disposed within the apparatus inone or more (i.e., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) rows of tworeceptacle holders per row. Thus, two receptacle holders may be disposedin a row either in thermal connection with, or thermally separated from,one another. In an exemplary embodiment, the apparatus 2100 includes sixrows of two receptacle holders per row.

As shown in FIGS. 58-60, the receptacle holder 2110 includes a plurality(i.e., two or more) of receptacle wells 2120 that are configured toreceive a receptacle 2130 (e.g., vial 464 or vial 1100) optionallycontaining a sample or reaction mixture 2140. For purposes ofexplanation, the surface of the receptacle holder into which thereceptacles 2130 are inserted will be referred to as the “top surface”2150 thereof. Likewise, the surface of the receptacle holder opposite tothe surface into which the receptacles 2130 are inserted will bereferred to as the “bottom surface” 2160. In an exemplary embodiment,each receptacle holder 2110 includes five or more (i.e., 5, 6, 7, 8, 9,10, or any whole integer between 1 and 10, or more) receptacle wells2120. In another exemplary embodiment, each receptacle holder 2110includes one to ten receptacle wells. In another exemplary embodiment,each receptacle holder includes three to six receptacle wells. In yetanother exemplary embodiment, each receptacle holder includes fivereceptacle wells. Each of the plurality of receptacle wells within arespective receptacle holder may be disposed in alignment with oneanother. In an exemplary embodiment, the receptacle wells 2120 aredisposed in a row extending along the length of the top surface 2150 ofthe receptacle holder 2110.

Exemplary materials from which a receptacle holder may be made include,but are not limited to, aluminum, titanium, copper, steel, magnesium,metal composites, metal alloys, ceramics, plastics, plastic composites,or any suitable thermally-conductive material.

As used herein, a receptacle well of the receptacle holder that is“configured to receive” a particular size or shape of receptacle refersto a receptacle well whose dimensions are substantially similar to thesize and shape of a receptacle 2130 (i.e., a sample tube) such that thereceptacle 2130 fits snugly within the receptacle well 2120, therebymaximizing contact between the surface of the receptacle well 2120 andthe receptacle 2130. In certain embodiments, this maximal contact refersto physical contact of the receptacle well 2120 with at least a portionof the receptacle 2130. In various embodiments, receptacles 2130 inaccordance with the present disclosure are individual reaction vesselsmade from suitable rigid or flexible materials, and shaped anddimensioned to fit within the receptacle wells of the apparatusdescribed herein. In other embodiments, two or more (i.e., 2, 3, 4, 5,or more) receptacles may be manufactured as a single unit configured tofit within a receptacle holder. Each receptacle 2130 may be closed orsealed to prevent contamination of and/or evaporation of the contentstherein, and/or to facilitate handling or transport of each receptacle.Such seals may be permanent or semi-permanent and may be fluid-tight. Incertain embodiments the seal comprises a cap or lid 2135.

Within each receptacle well 2120 is at least one through-hole 2170,which extends from an inner surface 2180 of the receptacle well to anouter surface of the receptacle holder. In an exemplary embodiment, thethrough-hole 2170 of a particular receptacle well 2120 extends from thebottom-center of inner surface 2180 of the receptacle well 2120 to thesurface of the receptacle holder 2110 that is opposite to the surface ofthe receptacle holder within which the receptacles 2130 are inserted(i.e., in this embodiment, the through-hole extends from the bottom ofthe receptacle well 2120 to the bottom surface 2160 of the receptacleholder 2110). In certain embodiments the diameter of the through-hole2170 is the same as that of the bottom 2190 of the inner surface 2180 ofreceptacle well 2120. In other embodiments, the through-hole 2170comprises a hole or opening having dimensions smaller than the bottom2190 of the inner surface 2180 of receptacle well 2120. In otherembodiments, the through-hole 2170 comprises a hole or opening havingdimensions the same size as, or larger than, the bottom 2190 of theinner surface 2180 of receptacle well 2120. The exact dimensions of thethrough-hole 2170 may vary, provided that the presence of thethrough-hole 2170 does not detrimentally affect the ability of thereceptacle holder 2110 to efficiently transfer heat to and from areceptacle 2130 held within the receptacle well 2120.

Thermal Element

As shown in FIGS. 61 and 62, positioned proximal to the receptacleholder is one or more thermal elements 2200 for altering a temperatureor temperatures of the receptacle holder 2110. As used herein, the term“thermal element” may include any known heating element for heating andcooling applications. In one embodiment, the thermal element is aresistive heating element, such as a thin metal film that is applied tothe receptacle holder 2110 by using well-known methods such assputtering or controlled vapor deposition. The heating element also canbe provided as a molded or machined insert (e.g., such as a cartridge)for incorporation into the receptacle holder 2110.

In an exemplary embodiment, the thermal element 2200 is a thermoelectricdevice, such as a “Peltier device,” which is generally constructed fromelectron-doped n-p semiconductor pairs that act as miniature heat pumps.When current is applied to the semiconductor pairs, a temperaturedifference is established, where one side becomes hot and the othercold. If the current direction is reversed, the hot and cold faces willbe reversed. Usually an electrically nonconductive material layer, suchas aluminum nitride or polyimide, is disposed over the substrate facesof the thermoelectric modules so as to allow for proper isolation of thesemiconductor element arrays.

As used herein, “altered temperature or temperatures” of the receptacleholder refers to the increase or decrease of the temperature of thereceptacle holder 2110. Often, the increase or decrease of thetemperature is determined relative to the ambient temperature. Includedin the term is the ability to individually adjust the temperature of oneor more receptacle wells 2120, while separately adjusting thetemperature of other receptacle wells within the same receptacle holder.Thus, the term may refer to uniformly raising/lowering the temperatureof all receptacle wells 2120 within a receptacle holder 2110 or mayrefer to altering a subset of the receptacle wells 2120 within a singlereceptacle holder 2110. As used herein, “ambient temperature” refers tothe temperature of a surrounding environment, which may include a fluid(e.g., air or liquid) or solid structure.

The thermal element 2200 may be electrically connected to a controllablepower source 2210 for applying a current across the element to alter thetemperature thereof. Control of the power source 2210 can be carried outby an appropriately programmed processor 2220 (such as a computer) whichreceives signals from one or more thermal sensors 2610 (see FIG. 61) inthermal communication with the receptacle holder 2110, as discussedbelow, and/or signals from another processor that controls the automatedprocess steps involved with temperature cycling processes.

The thermal element 2200 may be held in contact with a side surface 2115(see FIG. 58) of the receptacle holder 2110 by one or more supports2240, which may be positioned in sliding engagement with the receptacleholder 2110. As used herein, being positioned “in sliding engagement”refers to a non-fixed contact between adjacent surfaces of differentparts of the apparatus described herein. Thus, when the apparatus 2100includes two or more receptacle holders 2110, each of the two or morereceptacle holders are configured in sliding engagement with a support2240. As used herein, the term “support” refers to a rigid structure,which can be thermally-conductive. Exemplary materials from which asupport may be made include, but are not limited to, aluminum, titanium,copper, steel, magnesium, metal composites, metal alloys, ceramics,plastics, plastic composites, or any suitable rigid thermally-conductivematerial. Supports may also comprise a structure formed of, or from, acombination of materials, for example, plastic, metal (including alloysand composites), ceramic, or a combination of different types of one ormore of these materials.

As is known in the art, thermal elements may require a specific force toachieve adequate thermal contact with a component that is to be heated.For example, certain Peltier devices require a mounting force ofapproximately 150-300 psi to effectively transfer thermal energy to adevice. With reference to FIG. 62, the apparatus may include one or morecross-braces 2248 mounted to a support 2240, and exerting a force F1onto a front surface 2117 of a receptacle holder 2110. Force F1 issufficient to effect thermal transfer of energy from thermal element2200 to receptacle holder 2110. In certain embodiments, the apparatusincludes one cross-brace 2248 for each receptacle holder 2110. In otherembodiments, the apparatus includes one cross-brace 2248 per row ofreceptacle holders 2110. In such embodiments, the cross-brace generallyincorporates a portion or layer having low thermal conductivity as theportion that directly contacts the receptacle holder 2110. As discussedbelow, in other embodiments, a body 2300 having low thermal conductivityis used to exert the force required for thermal transfer of energy tothe receptacle holder 2110.

Cover

As shown in FIGS. 57, 58, and 64-68, the apparatus 2100 may also includea cover 2350 that is positioned in movable association with thereceptacle holder 2110. As can be expected, the cover 2350 is movablebetween an open position (FIG. 64) and a closed position (FIG. 65)relative to the receptacle holder 2110, and may be moved to any positionbetween open and closed, as necessary. In the open position, the cover2350 does not obstruct access to the receptacle wells 2120 within thereceptacle holder 2110 (see FIG. 63). When in the closed position, thecover 2350 will block and/or obstruct access to the receptacle wells2120. In addition, when closed, the cover 2350 may exert a force F2 ontoany receptacle within a receptacle well 2120 to seat or secure thereceptacle 2130 in the receptacle well 2120 (see FIG. 65). As discussedabove, because the receptacle well 2120 is configured to receive areceptacle 2130, the force F2 exerted by the cover 2350 serves to ensurethat the receptacle 2130 fits snugly within the receptacle well 2120,thereby allowing maximal contact between the inner surface 2180 of thereceptacle well 2120 and the receptacle 2130.

The cover 2350 may be made from any rigid or semi-rigid materialsuitable for exerting downward pressure onto a receptacle disposedwithin a receptacle well. Exemplary materials from which the cover maybe made include, but are not limited to, beryllium copper, spring steel,chrome vanadium, chrome silicon, phosphor bronze, stainless steel,aluminum, titanium, tungsten, metal alloys, metal composites, plastic,or any suitable rigid or semi-rigid material.

The cover 2350 may be movable by any suitable mechanical elementincluded in the apparatus. In one embodiment, the cover 2350 is hingedlyattached to the apparatus 2100 so as to enable movement between the openand closed positions. Attachment points include, but are not limited toany of the one or more supports of the apparatus or any suitablelocation within a housing containing the apparatus. As shown in FIG. 56,the cover 2350 may be fixedly attached to a rigid rotatable member 2352,which is in movable communication with one or more electric motors 2355.The rotatable member may be rotatably mounted to opposing sides of thehousing 2050 of the apparatus or opposing sides of additional supportmembers thereof, and span a length of the apparatus parallel to theorientation of one or more receptacle holders such that actuation of therotatable member 2352 results in the cover 2350 being moved into theopen or closed position relative to the one or more receptacle holders2110. In an exemplary embodiment, the rotatable member 2352 is acylindrical rod having a circular cross-section and an axis of rotationat the center thereof, as shown in FIG. 67, which is a sectional viewtaken along A′-A′ in FIG. 66. Exemplary materials from which the rigidrotatable member may be made include, but are not limited to, steel,titanium, aluminum, or any suitable rigid material. As used herein, theterm “rotatably mounted” refers to any mounting orientation that allowsthe rotatable member to rotate about its center axis.

The cover 2350 may comprise one or more (i.e., 1, 2, 3, 4, 5, 6, 7, 8,9, 10, or more) flexible extensions 2360 attached to and extendinglaterally away from, the rigid rotatable member 2352. Such flexibleextensions 2360 are configured to make contact with at least a portionof a receptacle 2130 disposed within the receptacle holder 2110 when thecover is in, approaching, or for a short distance after leaving, theclosed position. As contact is made between the flexible extensions 2360and at least a portion of the receptacle 2130, the flexible extensions2360 flex while applying force F2 directly to at least a portion of thereceptacle 2130. In an exemplary embodiment, the cover 2350 includes twoor more (i.e., 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) flexible extensions2360 extending in the same direction away from the rigid rotatablemember 2352. In certain embodiments, the flexible extensions 2360 extendlaterally away from the hinged attachment of the cover 2350 to theapparatus 2100. In frequent embodiments, the cover 2350 includes oneflexible extension 2360 per receptacle well 2120 of a receptacle holder2110. Also in frequent embodiments, one flexible extension 2360 of thecover 2350 may contact at least a portion of more than one receptacle2130 disposed within the receptacle holder 2110. Likewise, more than oneflexible extension 2360 may contact at least a portion of more than onereceptacle 2130 disposed within the receptacle holder 2110.

The cover 2350 of the present disclosure often comprises multiplecomponents, such as flexible extensions 2360, a rotatable member 2352,or other elements, as a single molded cover unit, or in multipleelements comprising the entire cover unit. For example, the flexibleextensions 2360 may be attached to the rotatable member 2352, or asingle material may comprise the rotatable member 2352 and the flexibleextensions 2360.

The apparatus 2100 may include a single cover 2350 in moveableassociation with all receptacle holders 2110 (not shown), or may includea single cover 2350 for each row of receptacle holders 2110, or mayinclude a single cover 2350 for each individual respective receptacleholder 2110. Movement of each cover 2350 may be actuated by an electricmotor 2355 disposed either within the apparatus 2100 or within thehousing 2050 in which the apparatus is located. When the apparatus 2100includes more than one cover 2350, each cover 2350 may be actuated byits own motor 2355, or more than one cover 2350 may be actuated by thesame motor 2355. As such, when the apparatus 2100 includes more than onecover 2350, each cover 2350 may move independent of the next and/or morethan one cover 2350 may be moved simultaneously. One of skill in the artwould appreciate that independent movement of multiple covers utilizinga single motor may be provided through, for example, appropriate cammingof its connection to each cover. The electric motor 2355 is electricallyconnected to a controllable power source 2210 for applying a currentthereto. Control of the power source 2210 can be carried out by anappropriately programmed processor 2370 (such as a computer) which mayreceive signals from another processor that controls the automatedprocess steps involved with temperature cycling processes.

With reference now to FIG. 68, there is provided a second exemplaryembodiment of an apparatus 2800 described herein. The description willbe provided based on the differences from the first exemplary embodimentdiscussed above. As such any reference to like elements should beunderstood as described above.

As shown in FIG. 68, the apparatus 2800 may also include a primary cover2840 that is fixedly positioned over the receptacle holder 2110. Theprimary cover 2840 may be formed with one or more (i.e., 1, 2, 3, 4, 5,6, 7, 8, 9, 10, or more) securing arms 2845 in direct alignment with andcircumventing each receptacle well 2120 of the receptacle holder 2110.In certain embodiments, the primary cover 2840 is formed with foursecuring arms 2845 in direct alignment with and disposed in asurrounding arrangement with each receptacle well 120 of the receptacleholder 2110. The securing arms 2840 are configured for securableattachment to at least a portion of the receptacle or cap 2135 that isattached to a receptacle 2130. Such securable attachment is analogous tothe force F2 exerted by the cover 2350, as discussed above, for ensuringthat the receptacle 2130 fits snugly within the receptacle well 2120,thereby allowing maximal contact between the inner surface 2180 of thereceptacle well 2120 and the receptacle 2130. The securing arms can bemade of any suitable material, including plastic, metal, or a metalcomposite.

The apparatus 2800 may further include a secondary cover 2850 fixedlypositioned over the primary cover 2840. The secondary cover 2850 may beformed with one or more (i.e., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more)releasing arms 2855, each in direct alignment and in sliding contactwith the securing arms 2845 of the primary cover. In variousembodiments, the securing arms 2845 of the primary cover include anangled surface 2847 upon which the corresponding releasing arm 2855 ofthe secondary cover 2850 may slide when actuated during an automatedprocess. The secondary cover 2850 may further include one or more (i.e.,1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) actuators 2860 that are fixedlyconnected to the releasing arms 2855, and are positioned such that whena force is applied thereon, the force is transferred from the actuator2860 to the releasing arms 2855, which in turn, press onto the angledsurface 2847 of the primary cover 2840 and release the securableattachment to the cap 2135 that is attached to a receptacle 2130.

It is therefore contemplated that the housing 2050 within which theapparatus 2800 is located will include at least one modified pipettor2900, as shown in FIGS. 69 and 70. As shown in FIG. 69, the modifiedpipettor 2900 is modified such that the plunger 2910 is slidinglyconnected to one or more limbs 2915, which are hingedly attached to thebody 2920 of the modified pipettor 2900. Thus, when the modifiedpipettor 2900 causes the plunger 2910 to be in a first position (asshown in FIG. 69), the one or more limbs 2915 are in a retractedposition such that a lower portions 2915 thereof are placed in closeproximity to the body 2920. When the modified pipettor 2900 causes theplunger 2910 to be in a lowered second position (as shown in FIG. 70),the one or more limbs 2915 are then moved into an extended position suchthat the lower portions 2915 thereof are moved away from the body 2920.

This modified pipettor 2900 is useful for engaging the secondary cover2850 and pressing on the secondary cover 2820 in a downward movementthat actuates the release of the securing arms 2845 by the physicalaction of the releasing arms 2855. When the releasing arms 2855 aredepressed in this manner, the securing arms 2845 are pulled axially awayfrom the receptacle 2130 and cap 2135, permitting its unencumberedrelease and lifting out by the pipettor. In such circumstances it isadvantageous that the securing arms maintain contact with, and depressin a radially outward manner, the releasing arms 2855 for the timeperiod required for the pipettor plunger 2910 to frictionally engage thereceptacle cap and to lift the receptacle and cap vertically clear ofthe securing arms 2845.

In certain embodiments, any of the apparatuses described herein will notinclude a cover or a mechanism to exert force F2 onto the cappedreceptacle 2130. In such embodiments, the receptacle 2130 fits snuglywithin the receptacle well 2120, thereby allowing maximal contactbetween the inner surface 2180 of the receptacle well 2120 and thereceptacle 2130 without the need for a force F2.

Optical Fibers

With reference now to FIGS. 72-74, the apparatus 2100 further includes aplurality of (i.e., more than one) optical fibers 2400 to provideoptical communication of a receptacle well with at least one of anexcitation signal source 2500 and an emission signal detector 2510 (seeFIG. 75). In one embodiment, the apparatus 2100 includes one opticalfiber 2400 per receptacle well 2120. Thus, when the apparatus 2100includes ten receptacles wells 2120, at least ten optical fibers 2400will be provided to establish optical communication between thereceptacle well 2120 and one or more excitation signal sources 500and/or one or more emission signal detectors 2510.

As used herein, an “optical fiber” refers to a flexible, transparentfiber made of glass or plastic that functions as a waveguide to transmitlight between the two ends (i.e., the first end and the second end) ofthe fiber. Typically, optical fibers include a transparent coresurrounded by an opaque cladding material with a lower index ofrefraction and low to no autofluorescence characteristics. It should beunderstood that an optical pathway or assembly comprising the opticalfiber may optionally include one or more filters, lenses, etc., tomodify and/or focus and excitation or emission signals passingtherethrough. Optionally, the apparatus 2100 may include an opticalinterface 2440 between the first end 2410 of each optical fiber 2400 andthe receptacle 2130 (see FIG. 75). Such optical interface 2440 mayinclude a filter, lens, nose, cap, or any other element having desiredoptical properties. However, it should be understood that in variousembodiments, the interface 2440 is not, and/or does not function as alens. Exemplary interfaces 2440 useful in the apparatus include, but arenot limited to, glass or plastic balls, noses or caps covering the firstend 2410 of the optical fiber 2400, or any suitable optically clearmaterial.

The first end 2410 of each of the plurality of optical fibers 2400 isdisposed outside, within, or extending through a through-hole 2170 ofthe receptacle well 2110, thereby providing optical communication with areceptacle well 2120, and/or a receptacle 2130 disposed within thereceptacle well 2120. When disposed within the receptacle well 2120, asshown in FIG. 72, the first end 2410 of the optical fiber 2400 may bemoveable within the through-hole 2170 of the receptacle well 2120relative to the inner surface 2180 thereof. In various exemplaryembodiments, a variety of means of movement of the first end 2410 of theoptical fiber 2400 within the through-hole 2170 are contemplated. Forexample, the first end 2410 of the optical fiber 2400 may extend intothe receptacle well 2120, and when a receptacle 2130 is placed withinthe well 2120, the receptacle 2130 contacts the first end 2410 of theoptical fiber 2400, thereby providing optical communication between thereceptacle 2130 and the optical fiber 2400. In an exemplary embodiment,the presence of a receptacle 2130 within the receptacle well 2120 willcause the optical fiber 2400 to move within the through-hole 2170 (e.g.,through the application of a direct force) in a direction opposite fromthe inner surface 2180 of the receptacle well 2120 such that thereceptacle 2130 can make maximal contact with the inner surface 2180 ofthe receptacle well 2120 while maintaining optical communication withthe optical fiber 2400, as shown in FIG. 74. In another embodiment, thedownward force F2 exerted by the cover 2350 and/or the flexibleextensions 2360 of the cover 2350 onto at least a portion of areceptacle 2130 disposed within a receptacle well 2120 causes theoptical fiber 2400 to move within the through-hole 2170 when thereceptacle 2130 contacts the optical fiber 2400. In such embodiments,the receptacle 2130 may apply a force F3 to the first end 2410 ofoptical fiber 2400 in substantially the same direction as the force F2being applied to the receptacle, which is disposed within the well suchthat the end 2410 of the optical fiber 2400 moves within the well 2120.

As shown in FIG. 75, the system may further include one or moreexcitation signal sources 2500 and one or more emission signal detectors2510 to which the second ends 2430 of the optical fibers 2400 of theapparatus 2100, 2800 included therein are in optical communication.Excitation signal sources 2500 and emission signal detectors 2510contemplated by the present disclosure include, but are not limited to,fluorometers, luminometers, spectrophotometers, infrared detectors andcharged-coupled devices. Each of these types of optical detectionsystems can be positioned within the housing of the apparatus 2100,2800, within the housing of the system, or within the overall housing ofthe biochemical analysis instrument, as appropriate. Multiple types ofsignal sources 2500 and signal detectors 2510 may be movably mounted ona platform to facilitate different detection methods for differentprocesses. The system may also include multiple detectors of the same ordifferent types for detecting signals emitted from different receptacles2130 simultaneously. As discussed above, though FIG. 75 depicts separateoptical fibers branching out to the excitation signal source 2500 andemission signal detector 2510, certain embodiments of the presentdisclosure utilize a single optical fiber (e.g., a light pipe) betweenthe excitation signal source 2500 and its corresponding emission signaldetector 2510.

Methods of Establishing Optical Communication

In another aspect, disclosed herein is provided a method forestablishing optical communication between a receptacle and anexcitation signal source and/or an emission signal detector within ahousing of the apparatus while allowing maximal contact between thesurface of the receptacle well and the receptacle (FIG. 76). Asdiscussed in detail above, the method includes providing a receptacle2130 to a receptacle well 2120 of a receptacle holder 2110 (step S110).Thereafter, a force F2 is applied to the receptacle 2130 or at least aportion of the receptacle 2130, such that the receptacle 2130 fitssnugly within the receptacle well 2120, thereby allowing maximal contactbetween the inner surface 2180 of the receptacle well 2120 and thereceptacle 2230 (step S120). While force F2 is being applied to at leasta portion of the receptacle 2130, movement of a first end 2410 of anoptical fiber 2400 is effected toward the inner surface 2180 of thereceptacle well 2120 (step S130). In such embodiments, the receptacle2130 may apply a force F3 to the optical fiber 2400 in substantially thesame direction as the force F2 being applied to the receptacle 2130, tothe first end 2410 of the optical fiber 2400, which is disposed withinthe receptacle well 2120 such that optical communication is establishedbetween the bottom 2138 of the receptacle 2130 and the first end 2410 ofthe optical fiber 2400 (step S140). As discussed above, movement of thefirst end 2410 of the optical fiber 2400 is coordinated with movement ofcover 2350 into the closed position. As such, the method may furtherinclude movement of the cover 2350 in coordination with the movement ofthe first end 2410 of the optical fiber 2400.

Another exemplary embodiment of the method for establishing opticalcommunication between a receptacle and an excitation signal sourceand/or an emission signal detector within a housing of the apparatuswhile allowing maximal contact between the surface of the receptaclewell and the receptacle is shown in FIG. 77. In this embodiment, themethod includes providing a receptacle 2130 to a receptacle well 2120 ofa receptacle holder 2110 (step S210). Thereafter, a cover 2350 is movedinto the closed position (step S220), thereby exerting a force F2 ontothe receptacle 130 or at least a portion of the receptacle 2130, suchthat the receptacle 2130 fits snugly within the receptacle well 2120,thereby allowing maximal contact between the inner surface 2180 of thereceptacle well 2120 and the receptacle 2130 (step S230). Prior to,during, or after movement of the cover 2350 into the closed position,movement of a first end 2410 of an optical fiber 2400 is effected towardand into contact with the seated receptacle 2130 (step S240). Uponcontact of the first end 2410 of the optical fiber 2400 with the closedend 2138 of the receptacle 2130, force F4 is exerted by the first end2410 onto the receptacle 2130. In such embodiments, the receptacle 2130may apply a force F3, which is greater than force F4, onto the first end2410 of the optical fiber 2400 in substantially the same direction asthe force F2. As such, optical communication is established between thefirst end 2410 of the optical fiber and the receptacle 2130, whileensuring maximal contact between the receptacle 2130 and the inner wall2180 of the receptacle well 2120 (step S250). As discussed above,movement of the first end 2410 of the optical fiber 2400 is coordinatedwith movement of cover 2350 into the closed position.

Often, the first end 2410 of each of the plurality of optical fibers2400, or an area 2420 proximal to the first end 2410 of each of theplurality of optical fibers 2400, is connected, directly or indirectly,to a respective through-hole 2170 of a receptacle well 2120 with aresilient element 2600, as discussed above. The resilient element 2600thereby compresses and/or deforms as the optical fiber 2400 moves withinthe through-hole 2170, and returns to its uncompressed and/or originalform when the optical fiber 2400 returns to its rest position.

Signal Detection Module

Detection, and, optionally, measurement, of emission signals fromemission signal sources, such as vials containing reaction materialsundergoing amplification as described above can be performed inaccordance with aspects of the present invention with a signal detectionmodule. In an exemplary aspect, signal detector 432 comprises an asignal detection module indicated by reference number 3100 in FIG. 78.The signal detection module 3100 includes an upright reformatter frame3150. Two signal detector heads 3200 are attached to a lower end of thereformatter frame 3150 and an interface plate 3160 is attached to anupper end of the reformatter frame 3150. In general, the reformatterframe includes sides 3152, 3154 which, in the illustrated embodiment,comprise generally vertical columns, and a base 3156 within which areformed a plurality of fiber-positioning holes 3158. Note that thedesignation of the reformatter frame 3150 as being upright or the sides3152, 3154 as being vertical is merely to provide a convenient referencewith respect to the orientation of the signal detection module 3100 asshown in FIG. 78, and such terms of orientation are not intended to belimiting. Accordingly, the signal detection module 3100 could beoriented at any angle, including vertical or horizontal, or any angletherebetween. The reformatter frame has a variety of purposes, includingorganizing and arranging a plurality of optical transmission fibers 3180between an excitation/emission area and a detection area in an optimumoptical pathway orientation. In particular embodiments the reformatteralso provides for controlled orientation of a plurality of opticaltransmission fibers 3180 between the fins of a heat sink to a detectionarea.

The signal detector head 3200 is shown in FIG. 79. The signal detectorhead 3200 may be attached to a reformatter frame 3150 and is constructedand arranged to index one or more signal detectors into operativepositions with respect to each transmission fiber disposed in afiber-positioning hole of the base of the reformatter frame. In theembodiment shown in FIG. 79, the signal detector head 3200 includes abase plate 3220 configured to be attached to the base 3156 of thereformatter frame 3150 and including a plurality of fiber tunnels 3226arranged in a configuration corresponding to the spatial arrangement offiber-positioning holes 3158 formed in the base 3156 of the reformatterframe 3150 so that each fiber tunnel 3226 will align with acorresponding one of the fiber-positioning holes 3158.

In general, the signal detector head is configured to move one or moresignal detectors to sequentially place each signal detector into anoperative position with respect to each transmission fiber 3180 todetect a signal transmitted by the transmission fiber. The signaldetector head 3200 further includes a detector carrier 3250, which, inthe illustrated embodiment, comprises a carousel that carries aplurality of signal detectors 3300 in a circular pattern. In theillustrated embodiment, the signal detector head 3200 includes sixindividual signal detectors 3300, each mounted on a printed circuitboard 3210 and each configured to excite and detect a different emissionsignal or an emission signal having different characteristics.

Further details of the signal detector head 3200 are shown in FIG. 80,which is a transverse cross-sectional view of the detector head 3200along the line XIII-XIII in FIG. 79. Each signal detector 3300 includesa detector housing 3302 within which are formed an excitation channel3304 and an emission channel 306, which, in the illustrated embodiment,are generally parallel to one another. An excitation source 3308, suchas an LED, is mounted on the printed circuit board 3210 at the base ofthe excitation channel 3304. An emission detector 3314, such as aphotodiode, is coupled to the printed circuit board 3210 and is disposedwithin the emission channel 3306.

The detector carrier 3350 further includes, positioned adjacent thesignal detector housing 3302, a filter plate 3264 having a centralopening 3276 formed therein and defining an annulus. Within the annulus,an emission filter opening 3282 and an excitation filter opening 3280are formed in alignment with the emission channel 3306 and theexcitation channel 3304, respectively, of each signal detector housing3302. An excitation lens 3310 and an excitation filter 3312 are disposedin the excitation opening 3280. Although a single excitation lens 3310and a single excitation filter 3312 are shown in FIG. 80, the signaldetector 3300 may include multiple excitation filters and/or multipleexcitation lenses. Similarly, an emission filter 3316 and an emissionlens 3318 are disposed in the emission opening 3282. Although a singleemission filter 3316 and a single emission lens 3318 are shown in FIG.80, the signal detector 3300 may include multiple emission lenses and/ormultiple emission filters.

The detector carrier 3250 further includes, adjacent the filter plate3264, a mirror plate 3260 having a central opening 3262 and defining anannulus. The annulus of the mirror plate 3260 has formed thereinopenings aligned with the emission opening 3282 and the excitationopening 3280 formed in the filter plate 3264 for each signal detector3300. A mirror 3320 is disposed in the mirror plate 3260 in generalalignment with the excitation channel 3304, and a dichroic filter 3322is disposed in the mirror plate 3260 in general alignment with theemission channel 3306. Mirror 3320 is oriented at an angle (e.g. 45°)with respect to the excitation channel 3304 so as to be configured toredirect a light beam.

The detector carrier 3250 further includes an objective lens plate 3252having a central opening 3256 formed therein and defining an annulus. Alens opening 3254 is formed through the annulus of the objective lensplate 3252 in general alignment with the emission channel 3306 of eachsignal detector 3300. An objective lens 3324 is disposed within the lensopening 3254.

The base plate 3220 is disposed adjacent the objective lens plate 3252and includes fiber tunnels 3226 formed about the perimeter thereof.Although base plate 3220 and objective lens plate 3252 are depicted asabutting one-another in FIG. 80, it is contemplated that there can be adesignated distance, forming an air gap, between the base plate 3220 andthe objective lens plate 3252. Also, while objective lens plate 3252 andmirror plate 3260 are depicted as abutting one-another in FIG. 80, it iscontemplated that there can be a designated distance, forming an airgap, between the objective lens plate 3252 and the mirror plate 3260.

The detector carrier 3250, comprising the objective lens plate 3252, themirror plate 3260, and the filter plate 3264, as well as the signaldetectors 3300 carried thereon, are rotatable with respect to the baseplate 3220 so that each objective lens 3324 associated with each of thesignal detectors 3300 can be selectively placed into operative alignmentwith one of the fiber tunnels 3226 disposed in the base plate 3220.Thus, in the illustrated embodiment having six signal detectors 3300, atany given time, six of the fiber tunnels 3226 are in operative, opticalalignment with one of the objective lenses 3324 and its correspondingsignal detector 3300.

Operation of the signal detector 3300 in an exemplary embodiment isillustrated schematically in FIG. 81. The detector 3300 shown is afluorometer that is constructed and arranged to generate an excitationsignal of a particular, predetermined wavelength that is directed at thecontents of a receptacle to determine if a probe or marker having acorresponding emission signal of a known wavelength is present. When thesignal detector head 3200 includes multiple fluorometers—e.g., six—eachfluorometer is configured to excite and detect an emission signal havinga different wavelength to detect a different label associated with adifferent probe hybridized to a different target analyte. When a morefrequent interrogation of a sample is desired for a particular emissionsignal, it may be desirable to incorporate two or more fluorometersconfigured to excite and detect a single emission signal on the signaldetector head 3200.

An excitation signal is emitted by the excitation source 3308. As notedabove, the excitation source may be an LED and may generate light at apredetermined wavelength, e.g. red, green, or blue light. Light from thesource 3308 passes through and is focused by an excitation lens 3310 andthen passes through the excitation filter 3312. As noted, FIG. 82 is aschematic representation of the signal detector 3300, and the focusingfunctionality provided by the excitation lens 3310 may be affected byone or more separate lenses disposed before and/or after the filterelement 3312. Similarly, the filter functionality provided by the filterelement 3312 may be affected by one or more individual filters disposedbefore and/or after the one or more lenses that provide the focusingfunctionality. Filter element 3312 may comprise a low band pass filterand a high band pass filter so as to transmit a narrow wavelength bandof light therethrough. Light passing through the excitation lens 3310and excitation filter element 3312 is reflected laterally by the mirror3320 toward the dichroic 3322. The dichroic 3322 is constructed andarranged to reflect substantially all of the light that is within thedesired excitation wavelength range toward the objective lens 3324. Fromthe objective lens 3324, light passes into a transmission fiber 3180 andtoward the receptacle at the opposite end thereof. The excitation signalis transmitted by the transmission fiber 3180 to a receptacle so as toexpose the contents of the receptacle to the excitation signal.

A label that is present in the receptacle and is responsive to theexcitation signal will emit an emission signal. At least a portion ofany emission from the contents of the receptacle enters the transmissionfiber 3180 and passes back through the objective lens 3324, from whichthe emission light is focused toward the dichroic 3322. Dichroic 3322 isconfigured to transmit light of a particular target emission wavelengthrange toward the emission filter 3316 and the emission lens 3318. Again,the filtering functionality provided by the emission filter 3316 may beaffected by one or more filter elements and may comprise a high bandpass and low band pass filter that together transmit a specified rangeof emission wavelength that encompasses a target emission wavelength.The emission light is focused by the emission lens 3318, which maycomprise one or more lenses disposed before and/or after the filterelements represented in FIG. 81 by emission filter 3316. The emissionlens 3318 thereafter focuses the emission light of the target wavelengthat the detector 3314. In one embodiment, the detector 3314, which maycomprise a photodiode, will generate a voltage signal corresponding tothe intensity of the emission light at the prescribed target wavelengththat impinges the detector.

Centrifuge

As shown in FIGS. 1, 5, and 6, centrifuge 588 can be located on theamplification processing deck 430 of the second module 400. In oneexemplary embodiment, the centrifuge 588 will centrifuge one or more (upto five in one embodiment) capped processing vials 464, 1100 at a time.In an exemplary embodiment, each vial is centrifuged before PCR toensure that sample material is concentrated primarily in the bottom ofthe processing vial 464, 1100 and to remove any air bubbles from thecontents of the vial 464, 1100, which can affect heat transfer andoptical transmission quality. The substance transfer pipettor 410 of thefront arm 408 places the capped vial 464, 1100 into the centrifuge 588at an access port indicated at reference number 589. After centrifugingis complete, the vial transfer arm 418 of the back arm 416 removes thecapped vial 464, 1100 from the centrifuge 588 at an access portindicated at reference number 587 and places it in the thermal cycler432. In an embodiment, the centrifuge configuration (e.g., by providingseparate ports 587, 589) allows the substance transfer pipettor 410(front arm 408) and the vial transfer arm 418 (back arm 416) toload/unload capped vials 464, 1100 simultaneously without colliding witheach other. As such, in one embodiment, the centrifuge not only performsits function of providing centrifugation of loaded vials, but alsofunctions as a vial transport mechanism by transporting capped vials464, 1100 from a position 589 accessible to the substance transferpipettor 410 to a position 587 where the capped vials 464, 1100 areaccessible to the vial transfer arm 418. In certain embodiments thesubstance transfer pipettor 410 is unable to access position 587 and thevial transfer arm 418 is unable to access position 589.

In addition, the centrifuge 588 may be configured to track theposition(s) of the loaded vial(s) within the centrifuge and determinewhen a vial is positioned at either access port 587, 589. For example, aturntable or other rotating structure on which the loaded vial(s) is(are) centrifuged may be driven by a stepper motor that may include arotary encoder for precise movement of the turntable and tracking motorcounts and/or the turntable or rotating structure may include arotational position indicator, such as a home flag sensor, configured toindicate one or more rotational positions or reference points.

In one exemplary embodiment, the maximum revolution speed of thecentrifuge is 3000 revolutions per minute, but other revolution speedsare contemplated based on, inter alia, the composition of the solutionbeing centrifuged and the time period required to provide adequatecentrifugation.

Receptacle Distribution System and Rotary Distributor

In one embodiment, the receptacle distributor, which is configured tomove a receptacle onto the receptacle distributor at a first location onthe second module, carry the receptacle from the first location to asecond location on the second module that is different from the firstlocation, and move the receptacle off the receptacle distributor at thesecond location on the second module, comprises a rotary distributor. Inan exemplary embodiment, the rotary distributor of the receptacledistribution system does not constitute a robotic pipettor, such assubstance transfer and handling device 402 described above, or othersubstance transfer device comprising a vial transfer arm that issupported on a structure for automatically moving the pipettor indifferent Cartesian directions (i.e., a x-y-z directions), but is also a3-axis robot designed to transport MRDs 160 and reagent packs 760between different components of the second module 400. In one exemplaryembodiment, rotary distributor 312 works by a hook and rail system inwhich an extendible and retractable hook pulls or pushes MRDs 160 orreagent packs 760 into or from a distributor head of the rotarydistributor 312. Within the distributor head, the MRD 160 or reagentpack 760 is supported and guided by rail and wall features within thehead. The rotary position of the distributor head is controlled andmonitored by a rotary encoder on the motor for position feedback and hasa home sensor. The distributor hook may be belt driven with home and endof travel sensors (e.g., slotted optical sensors, limit switches, etc.)The rotary distributor 312 is also configured for powered, vertical (orz-axis) motion of the distributor head for vertical translation of anMRD 160 or reagent pack 760. In one exemplary embodiment, the rotarydistributor 312 is configured to allow for at least 100 mm of z-axistravel. The distributor head may include an MRD/reagent pack presencesensor in the head. In one exemplary embodiment, the rotary distributoris configured to transfer an MRD 160 between any two modules of thesecond module 400 within four seconds. In certain embodiments, each axiscan make a full travel move in approximately one second.

Details of an exemplary receptacle distribution system are shown inFIGS. 27 and 28. In the illustrated embodiment, a receptacledistribution system 200 includes a frame 202 comprising legs 203,204 and205 extending between a bottom panel 208 and a top panel 206. Thereceptacle handoff station 602 is mounted on a handoff station bracket606 attached to the bottom panel 208 of frame 202 and will be discussedfurther below. Magnetic elution slots 620 and reagent pack loadingstations 640 are supported on a bracket 642 attached to legs 204 and 205of frame 202 and will be discussed further below. A rotary distributor312 is supported on a first upright wall 218 and a second upright wall220 within the frame 202.

Details of an exemplary rotary distributor 312 are shown in FIGS. 29-31.The exemplified rotary distributor 312 includes a distributor head 314defining a partial enclosure for holding an MRD 160 or reagent pack 760and a receptacle hook 318 configured to engage the manipulatingstructure 166 of an MRD 160 or the manipulating hook 764 of the reagentpack 760.

A hook actuator system 316 linearly translates the receptacle hook 318with respect to the distributor head 314 between an extended position,as exemplified in FIG. 30, and a retracted position, as exemplified inFIG. 29. The exemplified hook actuator system 316 includes a hookcarriage 320 to which the receptacle hook 318 is attached. A drive belt344 is attached to the hook carriage 320 by a screw and bracketindicated at 322. Drive belt 344 is carried on a drive wheel 334 andidler wheels 336, 338, 340, 342. Although exemplified using a drivebelt-based system, it is understood that other mechanisms, such asscrew-drive systems and linear piston actuators, are equally suited forthe hook actuator system

Referring to FIG. 31, which is a prospective of an opposite side of thedistributor head 314, a drive belt motor 370 having a rotary encoder 372is attached to the distributor head 314. Drive belt motor 370 is coupledto the drive wheel 334 that drives the drive belt 344 of the hookactuator system 316.

The hook actuator system 316 can include a belt tensioner 346 formaintaining proper tension in the belt 344. Belt tensioner 346 includesa pivoting idler wheel bracket 348 to which idler wheel 336 is attachedand which is pivotally attached to the distributor head 314 by a pivotscrew 352. A slot 350 is formed in an end of the pivoting idler wheelbracket 348, and a position lock screw 354 extends through the slot 350into the distributor head 314. A spring 356 bears against a portion ofthe pivoting idler wheel bracket 348. Tension in the belt 344 can beadjusted by loosening the position lock screw 354, thereby allowing thespring 356 to pivot the pivoting idler wheel bracket 348 and thus urgethe idler wheel 336 upwardly to create the proper tension in the drivebelt 344. When proper tension is achieved in the drive belt 344, theposition lock screw 354 can thereafter be retightened.

The hook carriage 320 includes a rail channel 324 that translates alonga hook carriage guide rail 330 attached to an upper, internal portion ofthe distributor head 314. The receptacle hook 318 is attached to a mount326 disposed between the rail channel 324 and the hook 318.

A hook home sensor, e.g., a slotted optical sensor or limit switch, maybe provided to indicate when the hook 318 is in the retracted, or“home,” position when a sensor flag extending from the mount 326 extendsinto the slotted optical sensor. Other types of sensors may be used forindicating a home position, such as proximity sensors, magnetic sensors,capacitive sensors, etc. The receptacle hook 318 and hook carriage 320are operatively coupled for electronic communication with the remainderof the rotary distributor 312 by means of a flexible cable 366 attachedat one end to the hook carriage 320 and at a printed circuit board orother connector located on the distributor head 314. Strain reliefs 368and 369 may be provided for securing the flexible cable 366 to thedistributor head 314 and the hook carriage 320, respectively.

FIG. 32 illustrates a manner in which a reagent pack 760 may betransported within the module 400 by means of the rotary distributor312. As shown in FIG. 32, the rotary distributor 312 may be configuredto receive and hold a reagent pack 760 that is pulled into thedistributor 312 by the manipulating hook of the rotary distributor 312with the bottom edge 765 of the pack 760 supported on a rail 373 formedon the inner walls of the distributor 312.

Similarly, FIG. 33 illustrates a manner in which an MRD 160 may betransported within the module 400 by the rotary distributor 312. Asshown in FIG. 33, the rotary distributor 312 may be configured toreceive and hold an MRD 160 that is pulled into the distributor 312 bythe manipulating hook of the rotary distributor 312 with the connectingrib structure 164 of the MRD 160 supported on a rail 373 formed on theinner walls of the distributor 312.

The receptacle distribution system 200 includes a distributor movingdevice configured to move the distributor head 314 in a circular path orin a vertical, linear path. More specifically, in one exemplaryembodiment, the distributor moving device includes a rotary drive system212 configured to move the distributor head 314 in a circular path andan elevation system 230 configured to move the distributor head 314 in avertical direction.

Details of an exemplary rotary drive system 212 are shown in FIGS. 27,28, 34, and 35. Although in certain embodiments, it is contemplated thatthe rotary drive system 212 is configured to freely rotate in 360°, itis understood that in at least certain embodiments the rotary drivesystem 212 is configured to rotate 180° between the two respectiveloading positions.

The first upright wall 218 and the second upright wall 220, on which thedistributor head 314 is supported, are mounted onto a turntable 214 thatis mounted for rotation about its central axis on the bottom panel 208of the frame 202. A motor 222, attached to the bottom panel 208 andhaving a rotary drive 224, such as a rotary drive gear, extending abovethe bottom panel 208, engages peripheral teeth of the turntable 214 sothat powered rotation of the motor 222 effects rotation of the turntable214, as well as the first and second upright walls 218, 220 and thedistributor head 314 supported thereon. Although exemplified as havingteeth configured to engage each other, it is understood that the rotarydrive 224 and the turntable 214 can engage each other without havingteethed parts. In such an embodiment, both the rotary drive and theturntable can be wheels with rubberized outer surfaces to facilitatetraction. Rotary motor 222 is preferably a stepper motor for providingprecise control of the rotation of the turntable 214 and preferablyincludes a rotary encoder 223 for providing rotational position feedbackto a control system controlling the rotary motor 222. Other means forrotationally coupling the distributor head 314 to the motor 222 areencompassed within this disclosure and include, for example, belt(s) andpulley(s), gear trains comprising one or more gears, drive shafts andworm gears, etc.

As shown in FIG. 35, a positional sensor 226, which may comprise aslotted optical sensor including an optical transmitter-receiver pair,provides a rotational position feedback signal of the turntable 214.Optical sensor 226 may be configured to detect a passing of one or morepositional flags on the turntable 214 for indicating one or morespecific rotational positions. Sensor 226 includes prongs, or portions,located above and below the turntable 214 and thus the positionalflag(s) may comprise one or more openings (e.g., 227) formed through theturntable. Passage of an opening between the portions of sensor 226located above and below the turntable 214 complete the optical signaltransmission between the transmitter and receiver portions of the sensor226 and thus generate a signal corresponding to the passage of theopening. Other types of sensors may be used for indicating particularrotational positions, including proximity sensors, magnetic sensors,capacitive sensors, etc.

A second optical sensor 228 may be provided below the turntable 214.Sensor 228 may comprise a slotted optical sensor including an opticaltransmitter-receiver pair for detecting the passage of one or moresensor flags (not shown) extending beneath the turntable 214 forindicating a rotational position. Other types of sensors may be used forindicating a home position, including proximity sensors, magneticsensors, capacitive sensors, etc.

Details of a distributor elevation system 230 are shown primarily inFIG. 35. The depicted elevation system 230 includes a threaded rod 232extending upwardly from the turntable 214 through a motor 234 andinternal thread drive 236 mounted to the distributor head 314 (see alsoFIG. 31). Rotation of the internal thread drive 236 by the motor 234causes the motor and the distributor head 314 to which it is attached totranslate up or down the threaded rod 232. A guide rail 238 extendsvertically up one edge of the second upright wall 220, and the motor 234is coupled to the guide rail 238 by a rail coupling 240. Alternatives tothe threaded rod and the internal thread drive for moving thedistributor head 314 vertically are encompassed in this disclosure andinclude, for example, a rack and pinion or a belt drive system.

Referring to the embodiment of FIGS. 27, 28, and 34, a sensor 246extends below the distributor head 314. As the distributor head 314 islowered by the elevation system 230, separate prongs of the sensor 246extend into openings 216 formed in the turntable 214. Sensor 246 may bea slotted optical sensor with the prongs thereof forming atransmitted-receiver pair. An optical signal between the spaced prongsis broken when the prongs enter the openings 216, thereby sending asignal to a control system that the distributor head 314 is at itslowermost position. Other types of sensors may be used for indicating adown position for the distributor head 314, including, for example,proximity sensors, magnetic sensors, capacitive sensors, etc.

Data and power are communicated between the rotary distributor 312 andthe module 400 by means of a coiled cable 244 that can accommodaterotation of the rotary distributor 312 with respect to the frame 202 by,for example, 180° in either direction.

To transfer an MRD 160, the distributor head 314 is rotated a fewdegrees by the rotary drive system 212 of the rotary distributor 312,the hook 318 is extended by the hook actuator system 316, and the head314 is rotated in an opposite direction to engage the manipulatingstructure 166 of the MRD 160. The distributor hook 318 is thenretracted, and the MRD 160 is coupled to the distributor head 314.Similarly, to transfer a reagent pack 760, the distributor head 314 isrotated a few degrees by the rotary drive system 212, the hook isextended by the hook actuator system 316, and the head 314 is thenrotated in the opposite direction to engage the manipulating hook 764 ofthe reagent pack 760. The distributor hook 318 is then retracted, andthe reagent pack 760 is pulled into the distributor head 314.

Receptacle Handoff Device

The receptacle handoff device 602 is configured to transfer areceptacle, such as the MRD 160, between the receptacle distributor 150of the first module 100 and the rotary distributor 312 of the secondmodule 400. Both the receptacle distributor 150 of the first module 100and the rotary distributor 312 of the second module 400 manipulate theMRD 160 using a hook or other similar device to engage the manipulatingstructure 166 of the MRD 160. Therefore, after the MRD 160 is disengagedby the receptacle distributor 150 of the first module 100, the MRD 160is positioned and oriented in such a manner as to present themanipulating structure 166 to the rotary distributor 312 of the secondmodule 400. The handoff device 602 performs this function.

Details of the handoff device 602 are shown in FIGS. 27, 28, 39, 40. Thereceptacle handoff device 602 comprises a receptacle yoke 604 configuredto receive and hold an MRD 160 placed into the yoke 604 by thereceptacle distributor 150 of the first module 100. The yoke 604 ismounted on a handoff device bracket 606, attached to and extending fromthe bottom panel 208 of the frame 202, so as to be rotatable about avertical axis of rotation. In one exemplary embodiment, the yoke 604 iscoupled to a handoff device motor 680 attached to the bracket 606. Motor680 may be a stepper motor for precise motion control and may include arotary encoder 682 for providing rotational position feedback of thereceptacle yoke 604 to a controller. A sensor 684, which may be aslotted optical sensor comprising an optical transmitter-receiver pair,is mounted to the bracket 606 and detects a home flag 686 extending fromthe yoke 604 for providing rotational position feedback. Other types ofsensors may be used for providing position or orientation feedback,including proximity sensors, magnetic sensors, capacitive sensors, etc.After the MRD 160 is placed in the yoke 604 by the receptacledistributor 150 of the first module 100 and the receptacle distributor150 disengages the MRD 160, the housing 604 is rotated to present themanipulating structure 166 of the MRD 160 to the rotary distributor 312of the second module 400.

Alternatively, the handoff device 602 may be passively actuated by therotary distributor 312. For example, the handoff device rotation may betied to the rotation of the rotary distributor 312 (e.g., via a cable,belt, gear, or other means) such that when the rotary distributor 312rotates to the handoff position, the handoff device 602 would spinaround to face the rotary distributor 312. When the rotary distributor312 rotates away from the handoff device 602, the handoff device 602would rotate back toward the receptacle distributor 150 of the firstmodule 100.

MRD Storage Station

As shown in FIG. 14, the MRD storage stations 608, 610, 612 are locatedon the receptacle processing deck 600 of the second module 400 and serveas temporary locations for MRDs in the second module 400. Storagestations 608, 610, 612 include a number of slots 614, each configured toreceive an MRD 160. The storage stations 608, 610, 612 are arranged inan arc, thereby accommodating the rotational path of motion of therotary distributor 312. Providing additional storage for MRDs withinsecond module 400 provides the advantage of enhancing workflow bypermitting flexibility in the timing that any particular MRD, orcontents thereof, is/are utilized within second module 400. This permitsMRDs that may arrive in second module 400 later to be processed out oforder, for example, to address urgent needs in a laboratory.

Although exemplified as having three MRD storage stations 608, 610, 612,it is understood that embodiments can be constructed having two or moresuch storage stations. Similarly, although exemplified as beingconfigured in an arc arrangement, it is understood that the distributor312 in certain embodiments does not rotate about an arc and that the arcarrangement is convenient for the rotary distributor 312 embodiment. Tothe extent that an alternate configuration of the distributor 312 isimplemented, the MRD storage stations similarly would match thealternate arrangement to maximize workflow of the system.

Magnetic Elution Slots/Reagent Pack Loading Stations

The magnetic elution slots 620 (two in the illustrated embodiment) andthe reagent pack loading stations 640 are supported on a bracket 642attached to frame 202. The purpose of each magnetic elution slot 620 isto hold an MRD 160 and apply magnetic force to the contents of the MRDto pull the magnetic beads to the side walls of each receptacle 162while the substance transfer pipettor 410 aspirates the eluate fluidfrom the receptacles 162.

Details of the magnetic elution slots 620 and the reagent pack loadingstations 640 are shown in FIGS. 36-38. Each magnetic elution slot 620comprises a block 622 within which is formed a slotted opening 624. AnMRD 160 placed within the slotted opening 624 is supported within theopening 624 by the connecting rib structure 164 of the MRD 160 restingon the top of bracket 642. The manipulating structure 166 extends out ofthe opening 624, and a cutout 632 in each side wall of the block 622enables the hook 318 of the rotary distributor 312 to move laterallyinto or laterally out of the MRD manipulating structure 166 of an MRD160 located within the slotted opening 624. The top of the MRD isuncovered, thus enabling pipettor access to the receptacles 162 of theMRD 160 held within the elution slot 620. Magnets 628 are attached to orembedded within one or both walls defining the slotted opening 624.Individual magnets 628 may be provided for each receptacle 162 of theMRD 160, as shown in FIGS. 37 and 38, or a single magnet may be providedfor a receptacle that comprises one or more individual receptacles.

The reagent pack loading stations 640 are defined by spaced-apart,hold-down features 644 extending above the bracket 642 and a backstop646 defining a back end of each reagent pack loading station 640. Areagent pack 760 is inserted between the hold-down features 644, under alateral flange, and is pushed into the loading station 640 until theback end of the reagent pack 760 contacts the backstop 646.

Reagent Pack Trash Chute

A reagent pack trash chute 428 is supported on the bracket 642. In anexemplary embodiment, reagent pack trash chute 428 includes an entrancestructure, defined by side walls 434, 436 and a top panel 438, throughwhich a reagent pack 760 is inserted into the trash chute 428. Sidewalls434, 436 are attached to the top of the bracket 642 and are bent orflared outwardly at their forward edges to provide a funneling entranceto the trash chute 428. Resilient tabs 442 extend down from the toppanel 438.

To discard a reagent pack 760, the rotary distributor 312 inserts thepack 760 into the trash chute 428 between the side walls 434, 436. Whenthe reagent pack 760 is inserted into the trash chute 428, there is aclearance between the top panel 438 and the top of the reagent pack 760.The resilient tabs 442 bear against the top of the reagent pack 760 andhold the reagent pack 760 down within the trash chute 428. The angle theresilient tabs 442 permits the reagent pack 760 to be pushed into the ofthe trash chute 428, but resists movement of the reagent pack 760 out ofthe trash chute.

When a subsequent reagent pack 760 is inserted into the reagent packtrash chute, it is pushed against the reagent pack 760 previouslyinserted into the trash chute 428, thereby pushing thepreviously-inserted pack further into the trash chute 428. A cut-out 648is formed in the bracket 642, so the previously-inserted pack 760eventually falls from the trash chute 428 and, guided by a guide ramp444 extending down from the bracket 642, into a trash bin located belowthe trash chute 428.

Reagent Pack Changer

Details of an exemplary reagent pack changer 700 are shown in FIGS.15-17. The purpose of the reagent pack changer 700 is to provide fullyindependent reagent pack loading and test execution whereby an operatormay place reagent packs in a reagent pack input device and/or removereagent packs 760 from the reagent pack input device while previouslyloaded reagent packs 760 are stored within a storage compartment, whichmay be temperature controlled, and are available for access by theinstrument independently of the status of the reagent pack input device.The reagent pack changer is configured to move reagent packs 760 betweenthe reagent pack input device and the storage compartment.

As shown in FIGS. 15-17, in one exemplary embodiment, the reagent packinput device comprises a reagent pack carousel compartment 702 which maybe pulled open from the second module 400 and which contains a rotatablereagent pack carousel 704. The pack carousel 704 includes a number ofreagent pack stations 706, each of which is adapted to receive and carrya reagent pack 760 and which are defined by radially inner dividers 708and radially outer dividers 710. As can be seen in FIGS. 15-17, thereagent pack stations 706 of the reagent pack carousel 704 are arrangedabout the outer perimeter of the reagent pack carousel 704, but theelongated reagent pack stations 706, and reagent packs 760 carriedthereby, are not oriented in a radial direction with respect to thecenter of the reagent pack carousel 704. Each reagent pack station 706is oriented at an angle (e.g. 5-20°) with respect to a true radialorientation. This configuration of reagent packs optimizes the placementof reagent packs 760 on the carousel 704, thereby enabling the reagentpack carousel 704 to carry the maximum number of reagent packs 760 andproviding access of identifiable indicia present on each reagent pack760 to the barcode reader 774.

A gap 712 between each inner divider 708—outer divider 710 pair enablesan operator to insert his or her fingers into the gap 712 to therebygrasp the sides of the reagent pack 760 for placing the reagent pack 760into the reagent pack station 706 or for removing the reagent pack 760from the reagent pack station 706. Each reagent pack station 706 of thereagent pack carousel 704 also includes an alignment block 714 at aradially inner end of the reagent pack station 706. The alignment blockwithin the rear recess 770 of the reagent pack 760 helps to maintain theproper alignment and position of the reagent pack 760 within the reagentpack station 706.

In some embodiments, the reagent pack carousel compartment 702 includesa carousel frame 716, preferably disposed on a track that enables theframe 716 to be slid into or out of the module 400 as a drawer. Theframe 716 includes a drawer front 720. The reagent pack carousel 704 isrotatably disposed within the frame 716, which may include a circularrecess 722 shaped so as to conform to the reagent carousel 704.

The reagent pack carousel 704 is motorized to effect powered rotation ofthe carousel. In one exemplary embodiment, the reagent pack carouselcompartment 702 may include a motor (not shown) that is coupled, forexample by a belt and pulley arrangement (not shown), to the reagentpack carousel 704 for powered rotation of the reagent pack carousel 704.The motor may be mounted to the reagent pack carousel frame 716 and movein and out with the reagent pack carousel compartment 702, connected tothe module 400 by a flex cable. The reagent pack carousel compartment702 may include one or more position sensors for detecting when thecarrousel is in an open or closed position and communicating acorresponding signal to the system controller. Such sensor(s) mayinclude optical sensors, proximity sensors, magnetic sensors, capacitivesensors, etc.

The reagent pack carousel compartment 702 may also include asoftware-controlled lock.

The reagent pack carousel compartment 702 can also include one or moresensors for tracking the positions of the reagent pack station 706. Forexample, the reagent pack carousel 704 may include a home flag, such asa tab and an optical sensor that detects the position of the tab at aspecified rotational position of the reagent pack carousel 704. Othertypes of sensors may be used for indicating a home position, includingproximity sensors, magnetic sensors, capacitive sensors, etc.Furthermore, the motor driving the reagent pack carousel 704 may be astepper motor including a rotary encoder for generating signalscorresponding to a rotational position of the reagent pack carousel 704.

The second module 400 may include a machine pack reader configured toread a machine code provided on each reagent pack 760 providinginformation regarding the reagent pack 760, such as the identity of theassay reagents carried within the reagent pack 760, manufacturer, lotnumber, expiration date, etc. The machine code may also include a uniqueidentifier specifically identifying that particular reagent pack 760.The machine code reader device may comprise a barcode reader 774configured to read a barcode label 772 disposed on the reagent pack 760.Barcode label 772 may be a two dimensional or one dimensional barcode. Ascanning slot 718 formed in the carousel frame 716 provides an openingthrough which the barcode reader 774 may read a label 772 on the reagentpack 760. Similarly, the orientation of the reagent pack 760 carried inthe pack station 706 of the pack carrousel 704, may be set at an anglewith respect to a true radial orientation, and the shape of the outerdividers 710, being generally trapezoidal in shape, creates a clearanceopening through which the barcode reader 774 can read the barcode label772 disposed on the reagent pack 760. Together with the rotary encoder,the barcode reader 772 provides an indication where each reagent pack760 is positioned within each reagent pack station 706 of the reagentpack carrousel 704. Although a barcode scanner is exemplified, the useof other technologies such as RFID and QR codes are contemplated.

Each reagent pack station 706 may include a station empty barcodedisposed on a side of each outer divider 710 that will be read by thebarcode reader 774 if a reagent pack 760 is not positioned within thereagent pack station 706.

In another exemplary embodiment, the reagent pack input device comprisesan alternative reagent pack carousel 730 shown in FIG. 18. Reagent packcarousel 730 is not carried on drawer be pulled out of the module 400,but instead, includes radially oriented reagent pack stations 732arranged about the perimeter of the reagent pack carousel 730 and isaccessible through a slot in front of the second module 400 which may becovered by a door that is openable by the operator. Powered rotation ofthe reagent pack carousel 730 may be provided by a carousel drive systemthat may include a motor 734 having an output drive wheel 736 that iscoupled to a drive pulley 739 of the carousel 730 by means of a drivebelt 738. Motor 734 may comprise a stepper motor having a rotaryencoder, and a home flag may be provided on the carousel 730 to detectand monitor the rotational position of the reagent pack carousel 730 andthus each reagent pack station 732.

FIG. 18 also shows an exemplary embodiment of a reagent pack storagecompartment represented by reference number 740. The storage compartment740 is disposed beneath the reagent pack carousel 730. In theembodiments described above, the reagent pack carousel compartment 702would be disposed within the module 400 above the storage compartment740 and would be movable with respect thereto.

In some embodiments, storage compartment 740 includes a housing 742 thatdefines a temperature controlled chamber therein. The desired storagetemperature may be as low as 4° C., but could be any temperature at orbelow ambient temperature, for example, 15° C. In some embodiments, thechamber of the storage compartment 740 further has a humidity controlmodule configured to control the humidity level of the air circulatingwithin the temperature controlled chamber. As part of this process, thehumidity control module is optionally equipped to collect condensedwater, and route it outside the cooled storage area for disposal.

Housing 742 may be insulated and may be cooled by Peltier devices thatcan be mounted directly onto the housing 742 or by Peltier devicescoupled to a heat cools a fluid, such as water or a refrigerant, whichis circulated around the housing 742. In one embodiment the storagecompartment 740 is cooled by two separate Peltier devices mounteddirectly onto the housing 742, each at different temperatures ortemperature ranges. In this embodiment the first Peltier device is heldat a temperature close to the freezing temperature of water. The secondPeltier device is provided at a location within the storage compartment740 distant or adjacent to that of the first Peltier device and isprovided at a temperature higher than that of the first Peltier device,e.g., 15° C. The second Peltier device is in operable communication witha temperature sensor within the storage compartment 740, positioned nearthe top of the storage compartment 740. The second Peltier device wouldoperate based on the measured temperature to maintain a predeterminedtemperature in the storage compartment 740. In this embodiment a fan maybe provided within the storage compartment 740 to cause air circulationwithin the storage compartment 740 through the fan, and past the firstand second Peltier device s. When air passes the first Peltier device ,which is held at a very low temperature, the air will cool, thusdecreasing its capacity to hold moisture which moisture will condensateon the Peltier device or another designated element. Therefore, thisdual Peltier device embodiment provides both a temperature and humiditycontrolled environment, which is beneficial for increasing theshelf-life of lyophilized reagents which are vulnerable to rapiddegradation in the presence of increased temperatures and atmosphericmoisture.

Other ways to cool and/or dehumidify the storage compartment 740 arecontemplated and the disclosure is not limited to the exemplifiedembodiments.

The housing 742 should be provided with a liquid collection and/ordrainage system for handling condensing liquid inside the housing 742.Such a system may, for example, include piping for directing thecollected condensate away from the housing 742 and to a drain or anevaporator.

A storage carousel 744 is rotatably mounted within the housing 742, forexample, on shaft 745. Storage carousel 744 includes a plurality of packstations 746 disposed around the perimeter thereof and positioned on oneor more levels of the carousel 744. In the illustrated embodiment,storage carousel 744 includes pack stations 746 on two levels, one abovethe other.

A carousel drive can power rotation of the storage carousel 744 withinthe storage compartment 740. The carousel drive may include a motor 748,which may be a stepper motor, having an output drive wheel 750 coupledby means of a drive belt 752 to a drive pulley 749 of the pack carousel744. Motor 748 may be located outside the housing 742—to keep heatgenerated by the motor 748 from heating the storage compartment 740—andthe drive belt 752 may extend through an opening in the housing 742.Alternatively, a drive pulley coupled to the carousel 744 may be locatedoutside the housing 740. The motor 748 may include a rotary encoder, andthe reagent pack carousel 744 may include a home flag for monitoring therotational position of each of the reagent pack stations 746 of the packcarousel 744.

Operation of the reagent pack changer 700 will now be described.

After the reagent packs 760 are placed in the reagent pack carousel 704or reagent pack carousel 730 of the pack input device, the barcode ofeach reagent pack 760 is read by a barcode reader 774 and the identityand other information provided by the barcode is associated with aparticular reagent pack station 706,732 of the reagent pack carousel704. Alternatively, the reagent packs 760 may be scanned externally ofthe module 400, for example, by a hand operated barcode scanner, beforethe reagent pack 760 being placed into the pack input device.

After reagent packs 760 have been placed into the reagent pack inputdevice, such as reagent pack carousel 704 or reagent pack carousel 730,pack carousel compartment 702 is shut or a door in front of the carouselaccess opening is closed. Next, the rotary distributor 312 removes oneor more reagent packs 760 from the reagent pack carousel 704, 730 andmoves the reagent pack 760 into a pack station 746 of the storagecarousel 744 of the storage compartment 740. As shown in FIG. 16, thecarousel frame 716 of the reagent pack carousel compartment 702 includesa reagent pack access slot 724 through which the rotary distributor 312can access the manipulating hook 764 of a reagent pack 760 disposedwithin the reagent pack station 706. To enable the rotary distributor312 to transfer reagent pack 760 between the reagent pack input carousel704 or 730, to the one or more levels of the storage carousel 744 of thestorage compartment 740, the rotary distributor 312 provides powered andcontrolled vertical, i.e., z-axis, motion. It is preferable that accessto the reagent pack access slot 724 by the rotary distributor 312 iscontrolled by a door when the reagent carousel 704 or 730 is temperaturecontrolled.

Once a reagent pack 760 is present in the storage compartment 740, it isavailable to be utilized in an amplification assay, for example, a PCRassay. When a sample is present requiring a particular assay, thecarousel of the storage compartment 740 rotates to a position where areagent pack 760 containing the specific unit dose reagents for thatparticular assay are accessible by the rotary distributor 312.Generally, such access will be through a door to maintain a tightlycontrolled temperature environment in the storage compartment 740. Thedistributor 312 will access the reagent pack 760 through the door andmove it to a reagent pack loading station 640 for reconstitution of oneor more lyophilized reagents contained on the reagent pack 760. When thereagent pack 760 is empty, or when the reagents of one or more wells onthe reagent pack 760 have been reconstituted and removed, thedistributor 312 will again move the reagent pack 760. If there arereagents remaining in the reagent pack 760, the distributor 312 willtransfer the reagent pack 760 back to the storage compartment 740. Ifthe reagent pack 760 contains no more reagents, or is otherwisedesignated as inappropriate for continued use (e.g., contaminated orexpired reagents), the distributor 312 will transfer the reagent pack760 to either a waste chute 426 or back to the reagent pack inputcarousel 704 or 730 for removal.

A further alternative for scanning each reagent pack 760 is for thedistributor 312 to present each reagent pack 760 to a barcode scanner aseach reagent pack is removed from the reagent pack input carousel andbefore placing the reagent pack 760 into the storage carousel 744.

Reagent identity control is maintained after the bar code (or othermachine code) is read on the reagent pack 760 by monitoring the positionof each reagent pack station 706, 732 of carrousel 704, 730 and eachreagent pack station 746 on the storage carrousel 744 and associatingthe reagent pack 760 identity—from the bar code—with the reagent packstation position.

The reagent pack carousels 704, 730 rotate independently of the storagecarousel 744 of the storage compartment 740 to allow an operator to loadand unload reagent packs 760 from the reagent pack carousel 704, 730while the module 400 (i.e., rotary distributor 312) independentlyaccesses reagent packs 760 stored in the storage carousel 744 for assayprocessing.

The reagent pack changer 700 preferably stores at least 28 to 30 or morereagent packs 760.

The second module 400 may further include an electrostatic generator toimpart an electrostatic charge for positioning and holding thelyophilized reagent 768 present in the reagent pack 760 at the bottom ofeach of the mixing wells 762 of the reagent pack 760. Though the reagent768 may be held at the bottom of the associated mixing well 768 with apreviously-imparted electrostatic charge, as noted above, the inclusionof a mechanism, such as a electrostatic generator, to actively pull thelyophilized reagent 768 down to the bottom of the mixing well 762 at thetime that the reagent is reconstituted will ensure its positioning inthe correct spot in the mixing well during reconstitution. In anembodiment, the electrostatic generator is positioned below the reagentpack loading station 640, 730. Alternatively, or in addition, anelectrostatic generator could be provided in the reagent pack carousel704, 730 present in the reagent pack loading drawer and/or the storagecarousel 744 present in the storage compartment 740. In such anembodiment, the electrostatic generator may be located under oroperatively coupled to the reagent pack station 706, 732 or the reagentpack station 746 below the reagent pack 760, as providing anelectrostatic generator within the storage compartment 740 will have anenhanced electrostatic effect due to the lower temperature and lowhumidity.

Storage/Expansion Module

Details of compartment 590 for storing accessories or to accommodatepossible expansion of the second module 400 are shown in FIGS. 5, 6, 14,and 15. In one exemplary embodiment, compartment 590 can house astandard 96 well plate. The plate is located such that both pipettorarms 408, 416 can access the 96 well plate location. The expansion spacehas access to the front (via a drawer mechanism) so that the operatorcan load and unload the plate. The expansion space can also be accessedfrom the side of the instrument. A drive system comprising, for example,a motor-driven belt, may be provided for translating a well plate orother container or component into or out of the second module 400.Compartment 590 can be utilized as an area for collecting cap/vialassemblies that have undergone a PCR and/or melting assay to provide forthe ability to perform additional assays (e.g., ELISAs) on the samplecontained in the cap/vial assembly. (A procedure for performing athermal melt analysis is disclosed by Wittwer et al. in U.S. Pat. No.8,343,754.) In certain embodiments an arrangement of cap/vial assembliesin the format of a 96 well plate has advantages if further processing ofthe samples is desired since the 96 well plate size is compatible with avariety of known sample processing and molecular assay instruments.

Instrument Theory of Operation

The first module 100 is used for the sample preparation portion of theamplification assay (i.e., minimally the steps for isolating andpurifying a target nucleic acid that may be present in a sample).Samples and TCR, which may include a magnetically-responsive solidsupports, are loaded onto the first module 100. Elution buffercontainers 502, 504 are loaded on the second module 400. The secondmodule 400 then automatically moves these containers into a space withinthe first module 100 that can be accessed by a substance transferdevice, for example, a reagent pipettor (not shown in FIG. 1), of thefirst module 100. Through information provided to the first module 100by, for example, an operator via a user interface or through automated,machine-readable information, such as a bar code, provided on the samplecontainer (not shown in FIG. 1), the first module recognizes that aparticular amplification assay will be initiated. To process samples,the receptacle distributor 150 of the first module 100 pulls a new MRD160 from an input queue 102 and places it into a sample dispenseposition within the first module 100. TCR and sample are transferredfrom a reagent container and sample tube, respectively, to eachreceptacle 162 the MRD 160 by a pipettor within the first module 100.The contents of the MRD 160 are then incubated for a prescribed periodat a prescribed temperature before the MRD 160 is transferred to amagnetic separation wash station 118, 120 for a magnetic wash procedure.

After the target capture process, the MRD 160 is moved by the receptacledistributor 150 to an amplification reagent dispense position in thefirst module 100. The substance transfer device of the first module 100then adds elution fluid to each receptacle 162 of the MRD 160 toseparate target (sample) material from the magnetic particles, and thefirst module 100 mixes the contents of each receptacle 162 beforesending the MRD 160 to the second module 400. The second module 400places the MRD 160 into one of a series of slots configured to hold MRD160. When signaled by the system controller, the second module 400 movesthe MRD 160 to a magnetic elution slot 620 to separate the elutednucleic acid material from the magnetic particles. The substancetransfer device 402, for example, a robotic pipettor, then initiates theamplification process. The pipettor 402 first dispenses oil to allprocessing vials 464, 1100 queued for use in testing. The pipettor 402then aspirates eluate/sample from the MRD 160, and then aspirates areconstitution reagent solution from a reconstitution reagent cartridgeor reservoir, dispensing them into a lyophilized-reagent well of reagentpack 760. The reconstitution reagent and a lyophilized amplificationreagent in the reagent well of reagent pack 760 may be drawn into andreleased from the pipette tip one or more times to ensure adequate andrapid reconstitution. The reconstituted amplification reagent ispipetted to the processing vial 464, 1100 and is then capped. Thereconstituted amplification reagent, sample, and oil may be drawn intoand released from the pipette tip one or more times to ensure adequatemixing. The capped vial 464, 1100 is transferred to the centrifuge andthen to the thermal cycler 432, such as thermal cycler 432 for PCRamplification and fluorometric detection.

Results may be displayed on an instrument monitor or user interface andeither printed or communicated to the LIS.

In an embodiment, the first module 100 is configured to perform one ormore isothermal nucleic acid amplification reactions on nucleic acidmaterial contained within an MRD 160. In one embodiment, such anisothermal process may be performed on the contents of the MRD 160before transporting the MRD 160 to the second module 400 to perform PCRon a portion of the MRD content material, as discussed above.Alternatively, after the MRD 160 is processed in the second module 400and an amount of eluate/sample is transferred from the MRD to one ormore vials 464, 1100 for performing PCR or other process(es) that thesecond module 400 is configured to perform. The MRD 160 may betransported back to the first module 100 to perform an isothermalnucleic acid amplification reaction on the remaining contents of the MRD160.

Exemplary Processes

Details of operation and a process embodying aspects of the presentdisclosure are shown in the flow charts of FIGS. 41-43. The followingprocesses are exemplary. Other processes may be performed and/or theprocesses shown herein and described below may be modified, e.g., byomitting and/or reordering certain steps.

A sample eluate preparation process that can be performed using thefirst module 100 and the second module 400 described above isrepresented by flow chart 800 in FIG. 41. In step S802 of method 800, areaction receptacle is moved to a location at which reaction materialscan be added to the receptacle. See, e.g., Clark et al. in U.S. Pat. No.8,309,036. For example, the receptacle distributor 150 of the firstmodule 100 moves an MRD 160 from the input device 102 to one of the loadstations 104, 106 or 108. See, e.g., Hagen et al. in U.S. PatentApplication Publication No. 2012/0128451.

In step S804 a substance transfer device of the first module 100transfers reaction materials to the receptacle. See, e.g., Buse et al.in U.S. Provisional Application No. 61/783,670. For example, a roboticpipettor of the first module 100 transfers a target capture reagent(“TCR”) (e.g., 500 μL), sample fluid (e.g., 360 μL), and target enhancerreagent (“TER”) (e.g., 140 μL) into each receptacle 162 of the MRD 160.

In step S806, the reaction materials added to the receptacle in stepS804 are mixed. For example, the TCR, sample fluid, and TER added to thereceptacles 162 of the MRD 160 are mixed by, for example, oscillatingthe MRD 160 at a high frequency (e.g., 60 seconds at 16 Hz).

In step S808, the receptacle is moved into an environment that willpromote the desired reaction. For example, the receptacle distributor150 removes the MRD 160 from the load station 104 and transfers the MRD160 to one of the incubators 112, 114, 116 (referred to as the ATBinding Incubator “ATB Incubator” in FIG. 41) to incubate the contentsof the MRD 160 at a prescribed temperature for a prescribed period oftime (e.g., 1800 seconds at 63° C.). Before moving the MRD 160 to anincubator, the MRD 160 may first be placed in one of the temperatureramping stations 110 (e.g., 300 seconds at 65° C.) to elevate thetemperature of the MRD 160 and its contents to a temperature that iscloser to that of the incubator into which the MRD 160 will betransferred so as to minimize temperature fluctuations within theincubator.

The desired reaction may require two or more incubations at differenttemperatures. Thus, in accordance with one implementation of thedisclosure, in step S810, the receptacle distributor 150 removes the MRD160 from one of the incubators and transfers the MRD 160 to anotherincubator (referred to as the “High Temp Incubator” in FIG. 41) that isat a different (e.g., higher or lower) temperature than the firstincubator to continue to incubate the contents of the MRD 160 at aprescribed temperature for a prescribed period of time (e.g., 600seconds at 43.7° C.).

In step S812, the receptacle distributor 150 removes the MRD 160 fromthe second temperature incubator and returns the MRD 160 to anotherincubator at a different temperature, which may be the same incubator(e.g., the “ATB Incubator”) the MRD 160 was placed into in step S808.

At the conclusion of the incubation step(s), it may be desirable to coolthe temperature of the contents of the receptacle, for example toterminate any reaction occurring within the receptacle. Thus, in oneexample, in step S814, the receptacle distributor 150 may remove the MRD160 from the incubator and transfer the MRD 160 to a chiller module 122(referred to as a “Chiller Ramp” in FIG. 41), maintained at apredetermined temperature.

Next, assuming the reaction performed within the receptacle includesimmobilizing a target nucleic acid on a magnetic-responsive solidsupport, a magnetic separation procedure is performed on the contents ofthe receptacle. Thus, in step S816, the receptacle distributor 150removes the MRD 160 from a chiller module 122 after a predeterminedperiod of time (e.g., 830 seconds), and transfers the MRD 160 to amagnetic parking station comprising magnets for attractingmagnetically-responsive solid support within each receptacle 162 to thewalls of the receptacles 162 to pull the solid support out ofsuspension. See, e.g., Davis et al. in U.S. Pat. No. 8,276,762. In stepS818, after a prescribed period of time within the magnetic parkingstation (e.g., 300 seconds), the receptacle distributor 150 removes theMRD 160 from the magnetic parking station and transfers the MRD 160 to amagnetic separation wash station 118 or 120. See, e.g., Hagen et al. inU.S. Patent Application Publication No. 2010/0288395. In step S820, amagnetic wash procedure is performed on the contents of the MRD 160placed into the magnetic wash station 118 or 120. One exemplaryembodiment of the magnetic separation procedure involves a numbermagnetic dwells during which the contents of the receptacle are exposedto a magnetic force for a predetermined period of time, and after eachmagnetic dwell, while the contents are still exposed to the magneticforce, the fluid contents are aspirated from the receptacle, leaving themagnetic particles behind in the receptacle. In one exemplaryembodiment, three magnetic dwells of 120 seconds each are performed. Atthe conclusion of each magnetic dwell, the magnetic force is removedfrom the contents of the receptacle. After each magnetic dwell, exceptthe last magnetic dwell, an amount of wash fluid (e.g., 1000 μL of washbuffer) is added to the receptacle to re-suspend the magnetic particlesbefore beginning the next magnetic dwell.

After the magnetic wash process is complete (e.g., after the lastmagnetic dwell followed by an aspiration of the non-magnetic fluidcontents of the receptacle), in step S822, the receptacle distributor150 retrieves the MRD 160 from the magnetic separation wash station 118or 120 and moves the MRD 160 to one of the load stations 104, 106 or108. In the load station, an amount of elution buffer (e.g., 50-110 μL)is transferred by, for example, a substance transfer device such as arobotic pipettor, from one of the elution containers 502, 504transferred into the first module 100 by the bulk reagent containertransport 550 of the bulk reagent container compartment 500 of thesecond module 400.

In some embodiments, it may be desirable to heat or incubate thecontents of the MRD 160 to improve the efficiency of the nucleic acidelution.

In step S824, following the addition of the elution buffer, the contentsof the MRD 160 are mixed by agitating the MRD 160.

In step S826, the MRD 160 is transferred from the first module 100 to amagnetic elution slot 620 in the second module 400. First, thereceptacle distributor 150 of the first module 100 retrieves the MRD 160from the load station 104, 106 or 108 and transfers the MRD 160 to anend of the transport track assembly 154 closest to the second module400. The distribution head 152 of the receptacle distributor 150 placesthe MRD into the receptacle handoff device 602 of the second module 400.The receptacle handoff device 602 then rotates the MRD 160 and presentsit to the rotary distributor 312. The rotary distributor 312 extends itshook 318 and engages the manipulation structure 166 of the MRD 160 byrotating a few degrees to place the hook 318 into the manipulationstructure 166 and then withdraws the hook 318 to pull the MRD 160 intothe distributor head 314 of the rotary distributor 312. The rotarydistributor 312 then rotates to align the MRD 160 carried therein withone of the magnetic elution slots 620 of the second module 400 (oroptionally MRD storage 608). The rotary distributor 312 then extends itshook 318 to push the MRD 160 into the magnetic elution slot 620 androtates a few degrees to remove the hook 318 from the manipulationstructure 166.

The process next proceeds to process 830 shown in FIG. 42.

Referring to FIG. 42, a reaction mixture preparation process isrepresented by flow chart 830. One or more of the steps of process 830may proceed in parallel with one or more of the steps of process 800shown in FIG. 41.

At step S832 the substance transfer pipettor 410 of the second module400 picks up a disposable tip 584 from a disposable tip tray 582 carriedin one of the tip compartments 580.

In step S834, the substance transfer pipettor 410 transfers an amount ofoil (e.g., 15 μL) from an oil container carried in the bulk reagentcontainer compartment 500 to one or more processing vials 464 held inthe cap/vial trays 460 of the processing cap/vial compartment 440.

In step S836, the substance transfer pipettor 410 moves to a trash chute426 to strip the disposable pipette tip 584 therefrom and discard thetip into the trash chute 426. Substance transfer pipettor 410 thenreturns to the disposable tip tray 582 and picks up another disposablepipette tip 584.

In step S838, substance transfer pipettor 410 transfers an amount ofreconstitution reagent (e.g., 20 μL) from a reconstitution reagentcontainer held in the bulk reagent container compartment 500 to a mixingwell 762 of a PCR reagent pack 760 that was previously transferred bythe rotary distributor 312 from the storage compartment 740 to a reagentpack loading station 640. In one embodiment, before the reconstitutionreagent is dispensed into the mixing well 762, the pipettor 410 performsa level sense at the foil 766 before piercing the foil 766 with thepipette tip 584. The level-sense performed on the foil of the reagentpack 760 to “calibrate” the height of the reagent pack 760 relative tothe pipettor. Generally, the pipettor 410 is configured to extend thepipette tip to the bottom of the mixing well for more accurate reagentaspiration.

In step S840, the fluid within the mixing well 762 is mixed to dissolvethe lyophilized reagent 768. In one example, the substance transferpipettor 410 mixes the fluid within the mixing well 762 by alternatelyaspirating the fluid into the pipette tip 584 and dispensing the fluidback in the well 762 one or more times to dissolve the lyophilizedreagent 768.

In step S842, the substance transfer pipettor 410 transfers an amount,(e.g., 20 μL) of the reconstituted reagent from the mixing well 762 ofthe PCR reagent pack 760 (referred to as “Mastermix” in FIG. 42), into avial 464. A PCR master mix provides the key ingredients necessary forperforming PCR in a premixed and optimized format. Included in themaster mix are Taq DNA polymerase, deoxynucleoside triphosphates(dNTPs), and magnesium chloride (MgCl₂). Not typically included are theforward and reverse primers.

In step S844, the substance transfer pipettor 410 moves to the trashchute 426 and strips the pipettor tip 584 into the trash chute. Thesubstance transfer pipettor 410 then moves to the disposable tip tray582 and picks up a new disposable pipette tip 584.

Block “B” in FIG. 42 represents the integration of process 800 shown inFIG. 41 with process 830 shown in FIG. 42. An MRD 160 containing asample mixture (which, in this exemplary embodiment, was purified in amagnetic separation procedure) and an elution buffer is held in amagnetic elution slot 620, having been placed there in step S826 ofprocess 800. In one embodiment, the MRD 160 is held in the magneticelution slot 620 for dwell period of at least 120 seconds.

In step S846 of process 830, the substance transfer pipettor 410transfers an amount of eluate (e.g., 5 μL) from the MRD 160 held in theelution slot 620 to the processing vial 464 to which oil and reagentwere added in steps S834 and S842, respectively.

In step S848, the substance transfer pipettor 410 moves back to thetrash chute 426 and strips the disposable pipette tip 584 into the trashchute.

The process now proceeds to process 850 shown in FIG. 43.

Referring to FIG. 43, a process for performing an automated biologicalprocess, such as a PCR reaction, is represented by flow chart 850. Block“C” in FIG. 43 represents the integration of process 830 shown in FIG.43 with process 850 shown in FIG. 43.

In step S852, the substance transfer pipettor 410 picks up a processingvial cap 476 from the cap well 440 of the cap/vial tray 460 by insertingthe pipettor probe 422 (without a disposable pipette tip thereon) intothe cap 476 as shown in FIG. 23 (see FIG. 26, which shows an alternativecap 1200 and vial 1100 combination). The substance transfer pipettor 410then picks up the cap 476, which is held onto the pipettor probe 422 byfriction, and inserts the cap 476 into the processing vial 464 held inthe processing vial well 474 until the cap 476 locks with the vial 464to form a cap/vial assembly (see FIG. 25 or FIG. 55).

In step S854, the substance transfer pipettor 410 transfers the cap/vialassembly held to the pipettor probe 422 by friction to the centrifuge588, where a stripping device removes the cap/vial assembly from thepipettor probe 422 to deposit the cap/vial assembly into the centrifuge588.

In Step 856, following a specified period of time in the centrifuge, thevial transfer arm 418 inserts its pipettor probe 422 into the cap 476 ofthe cap/vial assembly held in the centrifuge 588 and removes thecap/vial assembly from the centrifuge 588 and transfers the cap/vialassembly to an incubator module, such as the thermal cycler 432. Astripping device removes the cap/vial assembly from the pipettor probe422 of the vial transfer arm 418.

In step S858, an incubation process is performed. The incubation processmay include PCR thermal cycling comprising multiple cycles oftemperatures varying between 95° C. for denaturation, 55° C. forannealing, and 72° C. for synthesis. During the thermal cycler processan emission signal from the contents of the processing vial may bemonitored. For example, fluorescence monitoring at one or more coloredwavelengths during each PCR cycle may be measured using a signaldetecting device, such as a fluorometer, operatively integrated with thethermal cycler 432. Periodic fluorescence intensity measurements at eachwavelength may be made at regular intervals to generating fluorescencetime series data for later processing and analysis.

In step S860, following the PCR process of step S858, the vial transferarm 418 retrieves the cap/vial assembly from the thermal cycler 432 andtransfers the cap/vial assembly to a trash chute 424 where the cap/vialassembly is stripped from the pipettor probe 422 into the trash chute424, or the cap/vial assembly is transported to an output reagent pack760 in the storage/expansion module.

In some embodiments, diagnostic system 10 can be used to perform two ormore assays that include nucleic acid amplification reactions thatrequire different reagents, including one or more unit-dose reagents.FIG. 44 illustrates a method of using diagnostic system 10, whichincludes first module 100 and second module 400, according to one suchembodiment.

At step 862, a plurality of samples is loaded in diagnostic system 10. Afirst sample subset of the plurality of samples has been designated forat least one assay, and a second sample subset of the plurality ofsamples has been designated for at least one different assay. In someembodiments, barcodes on the sample receptacles indicate the appropriateassay, and in other embodiments, the assay is entered manually into thesystem by an operator using a user-interface of diagnostic system 10.

In some embodiments, a first assay comprising a first nucleicamplification reaction has been designated for the first sample subset.For example, the first nucleic amplification reaction can be PCR, andthe target nucleic acid can be a nucleic acid associated with aparticular virus or organism, for example. In some embodiments, thefirst nucleic amplification reaction uses a unit-dose reagent stored andoperatively accessible within the diagnostic system 10. For example, thefirst nucleic amplification reaction can be PCR or any other desiredthermal cycling reaction that can be performed by second module 400 ofdiagnostic system 10.

In some embodiments, a second assay comprising a second nucleicamplification reaction will be designated for the second sample subset.The second nucleic amplification reaction may be the same or a differentnucleic acid amplification reaction than the first nucleic acidamplification reaction of the first assay, but the reagent used in thesecond nucleic amplification reaction may target a different nucleicacid than the target of the first reagent used in the first assay insome embodiments. In some embodiments, the second nucleic amplificationreaction can be PCR or any other desired thermal cycling reaction thatis performed, for example, by second module 400 of diagnostic system 10.In some embodiments, the second nucleic amplification reaction is TMA orany other isothermal reaction that is performed, for example, by firstmodule 100 of diagnostic system 10. The reagent used for the secondassay can be a unit-dose reagent different than the unit-dose reagentused for the first assay, a bulk reagent, or both. For example, if thesecond nucleic amplification reaction is PCR, the second reagent used inthe second assay can be a unit-dose reagent, and if the second nucleicamplification reaction is TMA, the second reagent used in the secondassay can be a bulk reagent. In some embodiments, the second unit-dosereagent, the first bulk reagent, or both are stored and operativelyaccessible within diagnostic system 10.

Each of the first and second assays has a temporal workflow scheduleassociated with the respective assay. In some embodiments, at step 864,the diagnostic system 10 coordinates the schedule for performing thefirst assay with the schedule for performing the second assay such thatuse of resources of the diagnostic system is maximized For example, thefirst assay schedule may require use of one of the substance transferdevices, and the second assay schedule may also require use of the samesubstance transfer device. Diagnostic system 10 can be configured toshift one or both of schedules such that once the first assay isfinished with the substance transfer device, the substance transferdevice can be used for the second assay. Such coordination increasesthroughput and minimizes processing time.

At step 866, diagnostic system 10 performs the first assay on the firstsample subset. At step 868, diagnostic system 10 begins to perform thesecond assay on the second sample subset. Accordingly, diagnostic system10, which stores and provides operative access to the first unit-dosereagent used in the first assay and at least one of the second unit-dosereagent or the first bulk reagent used in the second assay, performsboth steps 866 and 868 according to an embodiment. In some embodiments,step 868 starts while step 866 is being performed—the diagnostic systemcan simultaneously perform the first assay and the second assay. In someembodiments, during steps 866 and 868 when the respective assays requirea unit-dose reagent, for example, for a PCR assay, diagnostic system 10verifies whether a reagent pack 760 containing the required reagent ispositioned at one of the loading stations 640. If not, the distributorsystem replaces a reagent pack 706 located at the loading station 640with a reagent pack 760 containing the unit-dose reagent needed for therequested assay. In some embodiments, step 868 starts after step 866 iscompleted. And in some embodiments, although step 868 can start afterstep 866, step 868 can be completed before step 866 is completed.

In some embodiments, diagnostic system 10 can alternate between step 866and 868. For example, diagnostic system 10 can perform the first assayon a first sample of the first sample subset, and then perform thesecond assay on a first sample of the second sample subset. Diagnosticsystem 10 can then switch back to step 866 and perform the first assayon a second sample of the first sample subset.

In some embodiments, the first assay and the second assay each comprisepreparing the respective sample subsets using a second bulk reagentdifferent than the first bulk reagent that may be used in the secondnucleic acid amplification reaction. For example, each sample of thefirst and second sample subsets can be prepared according to process 800described above referencing FIG. 41.

In some embodiments, the first sample subset and the second samplesubset comprise different samples. In some embodiments, the first samplesubset and the second sample subset comprise the same samples. In suchembodiments, multiple assays, for example, the first and second assaysexplained above, are performed on the same samples.

In some embodiments, steps 866 and 868 are performed without additionalequipment preparation (for example, wiping down the equipment ofdiagnostic system 10), reagent preparation (replacing reagent bottlesstored in diagnostic system 10), and consumable preparation (replacingempty tip trays).

Hardware and Software

Aspects of the disclosure are implemented via control and computinghardware components, user-created software, data input components, anddata output components. Hardware components include computing andcontrol modules (e.g., system controller(s)), such as microprocessorsand computers, configured to effect computational and/or control stepsby receiving one or more input values, executing one or more algorithmsstored on non-transitory machine-readable media (e.g., software) thatprovide instruction for manipulating or otherwise acting on the inputvalues, and output one or more output values. Such outputs may bedisplayed or otherwise indicated to an operator for providinginformation to the operator, for example information as to the status ofthe instrument or a process being performed thereby, or such outputs maycomprise inputs to other processes and/or control algorithms. Data inputcomponents comprise elements by which data is input for use by thecontrol and computing hardware components. Such data inputs may comprisepositions sensors, motor encoders, as well as manual input elements,such as graphic user interfaces, keyboards, touch screens, microphones,switches, manually-operated scanners, voice-activated input, etc. Dataoutput components may comprise hard drives or other storage media,graphic user interfaces, monitors, printers, indicator lights, oraudible signal elements (e.g., buzzer, horn, bell, etc.).

Software comprises instructions stored on non-transitorycomputer-readable media which, when executed by the control andcomputing hardware, cause the control and computing hardware to performone or more automated or semi-automated processes.

While the present disclosure has been described and shown inconsiderable detail with reference to certain illustrative embodiments,including various combinations and sub-combinations of features, thoseskilled in the art will readily appreciate other embodiments andvariations and modifications thereof as encompassed within the scope ofthe present disclosure. Moreover, the descriptions of such embodiments,combinations, and sub-combinations is not intended to convey that thedisclosure requires features or combinations of features other thanthose expressly recited in the claims. Accordingly, the presentdisclosure is deemed to include all modifications and variationsencompassed within the spirit and scope of the following appendedclaims.

1. A system for performing a nucleic acid amplification assay, thesystem comprising: one or more receptacle holders, each receptacleholder being formed from a thermally-conductive material and comprisingone or more receptacle wells, wherein each receptacle well conforms to alower portion of a vial, and wherein each receptacle holder includes athrough-hole extending from a bottom-center of an inner surface of eachwell to a bottom outer surface of the receptacle holder; one or morethermal elements positioned proximal to each receptacle holder foraltering a temperature or temperatures of the one or more receptacleholders; and a signal detection module in optical communication witheach of the one or more receptacle wells via the through-hole of eachreceptacle well, wherein the signal detection module is configured todetect an optical emission signal emitted from a fluid contained in avial supported by any of the receptacle wells, and wherein the signaldetection module is configured to generate an excitation signal that isdirected through the through-hole of a receptacle well and to detect anoptical emission from a content of the vial contained in the respectivereceptacle well and through the through-hole of the respectivereceptacle well, wherein at least one the receptacle wells supports acapped vial, the capped vial comprising a vial containing a fluid and anopaque cap in sealing engagement with an open end of the vial, whereinthe fluid contains reagents for performing a nucleic acid amplificationassay, wherein the lower portion of the vial is contained within the atleast one receptacle well, and wherein the cap is situated above a topsurface of the corresponding receptacle holder.
 2. The system of claim1, wherein each capped vial comprises one of the caps engaged with therespective vial in a frictional fit.
 3. The system of claim 2, whereinan outer surface of a lower portion of the cap of each capped vial is insealing engagement with an inner surface of an upper portion of therespective vial.
 4. The system of claim 1, wherein each cap isconfigured for inter-locking engagement with the respective vial.
 5. Thesystem of claim 4, wherein each vial comprises a lip circumscribing theopen end, wherein each cap comprises one or more locking arms extendingtoward a lower portion of cap, and wherein the one or more locking armsare configured for inter-locking engagement with the lip of a respectivevial.
 6. The system of claim 1, wherein one of the one or more thermalelements are positioned proximal to a side surface of a respectivereceptacle holder, and wherein the thermal element provides thermalenergy through the respective receptacle holder to each of thereceptacle wells of the respective receptacle holder.
 7. The system ofclaim 1, wherein the one or more thermal elements are configured andcontrolled to cyclically vary the temperature of the one or morereceptacle holders.
 8. The system of claim 1, wherein the signaldetection module comprises an excitation signal source and an emissionsignal detector, and the system further comprises a plurality of opticalfibers, each optical fiber comprising a first end and a second end,wherein the first end is in optical communication with one of thereceptacle wells through the through-hole of the well, and wherein thesecond end is in optical communication with at least one of theexcitation signal source and the emission signal detector.
 9. The systemof claim 8, wherein the excitation signal source is configured togenerate an excitation signal by generating a light at a predeterminedwavelength.
 10. The system of claim 9, wherein the emission signaldetector is configured to detect the optical emission signal byreceiving an optical emission from the fluid contained in the respectivevial and generating a voltage signal corresponding to an intensity ofthe received optical emission.
 11. The system of claim 8, wherein thesecond end of each optical fiber is in optical communication with theexcitation signal source and the emission signal detector.
 12. Thesystem of claim 8, wherein the excitation signal source is configured togenerate an excitation signal by generating a light at a predeterminedwavelength, and wherein the emission signal detector is configured todetect the optical emission signal by receiving an optical emission fromthe fluid contained in the respective vial and generating a voltagesignal corresponding to an intensity of the received optical emission.13. The system of claim 1, wherein the opaque cap has low to noautofluorescence.
 14. The system of claim 1, wherein the system does notinclude a cover configured to extend over the one or more receptacleholders.
 15. The system of claim 14, wherein the system is containedwithin a housing of an instrument.
 16. The system of claim 1 furthercomprising a cover corresponding to each receptacle holder, wherein thecover is configured to move between an open position and a closedposition relative to a respective receptacle holder.
 17. The system ofclaim 16, wherein the cover comprises a rigid element and one or moreflexible extensions attached to, and extending laterally away from, therigid element, wherein each flexible extension is associated with arespective receptacle well and is configured to apply a force to arespective capped vial when the cover is in the closed position, therebysecuring the respective capped vial within the respective well.
 18. Thesystem of claim 1 further comprising a primary cover fixedly positionedover a respective receptacle holder, wherein the primary cover comprisesone or more securing arms, each securing arm being configured forsecurable attachment to at least a portion of a respective cap, and asecondary cover fixedly positioned over the primary cover, wherein thesecondary cover comprises one or more releasing arms in alignment withand in sliding contact with the securing arms of the primary cover. 19.The apparatus of claim 1 further comprising a cover configured to moverelative to the receptacle holder between an open position and a closedposition, wherein in the open position, the cover does not obstructaccess to the receptacle wells, and wherein in the closed position, thecover blocks access to the receptacle wells of the receptacle holder.20. The apparatus of claim 19, wherein in the closed position, the coverdoes not exert force on the capped vial disposed in a receptacle well ofthe receptacle holder.
 21. The system of claim 1 further comprising: arobotic pipettor having a probe, wherein the cap of each capped vialcomprises an upper portion configured for removable engagement with theprobe of the robotic pipettor; and a centrifuge configured to receivethe capped vial, wherein the robotic pipettor is configured to transferthe capped vial to a first location of the centrifuge.
 22. The system ofclaim 21 further comprising a vial transfer arm configured for removableengagement with the upper portion of the cap, and wherein the vialtransfer arm is further configured to transfer the capped vial from asecond location of the centrifuge to one of the receptacle wells of thereceptacle holder, the first and second locations of the centrifugebeing different locations.
 23. The system of claim 1, wherein thenucleic acid amplification assay is a real-time amplification assay, andwherein the reagents are for performing the real-time amplificationassay.
 24. A method for a nucleic acid amplification assay, the methodcomprising the steps of: (A) with a robotic pipettor, dispensing a fluidinto a vial, the fluid containing reagents for performing a nucleic acidamplification assay; (B) engaging an opaque cap with a probe of therobotic pipettor for removably securing the cap to the probe; (C) withthe robotic pipettor, moving the cap secured to the probe into an openend of a vial and securing the cap to the vial to form a capped vial;(D) moving the capped vial into a receptacle well of a receptacleholder, wherein a lower portion of the vial is contained within thereceptacle well, and wherein the cap is situated above a top surface ofthe receptacle holder; (E) while the capped vial is in the receptacleholder, subjecting the fluid to temperature conditions for performingthe nucleic acid amplification assay; and (F) while the capped vial isin the receptacle holder, detecting an optical emission signal from thefluid through a through-hole extending from a bottom-center of an innersurface of the well beneath the vial to a bottom outer surface of thereceptacle holder, the intensity of the optical emission beingindicative of the presence or amount of an analyte in the fluid.